def main(): """ NAME lowrie.py DESCRIPTION plots intensity decay curves for Lowrie experiments SYNTAX lowrie -h [command line options] INPUT takes SIO formatted input files OPTIONS -h prints help message and quits -f FILE: specify input file -N do not normalize by maximum magnetization -fmt [svg, pdf, eps, png] specify fmt, default is svg -sav save plots and quit """ fmt, plot = 'svg', 0 FIG = {} # plot dictionary FIG['lowrie'] = 1 # demag is figure 1 pmagplotlib.plot_init(FIG['lowrie'], 6, 6) norm = 1 # default is to normalize by maximum axis if len(sys.argv) > 1: if '-h' in sys.argv: print(main.__doc__) sys.exit() if '-N' in sys.argv: norm = 0 # don't normalize if '-sav' in sys.argv: plot = 1 # don't normalize if '-fmt' in sys.argv: # sets input filename ind = sys.argv.index("-fmt") fmt = sys.argv[ind + 1] if '-f' in sys.argv: # sets input filename ind = sys.argv.index("-f") in_file = sys.argv[ind + 1] else: print(main.__doc__) print('you must supply a file name') sys.exit() else: print(main.__doc__) print('you must supply a file name') sys.exit() data = pmag.open_file(in_file) PmagRecs = [] # set up a list for the results keys = ['specimen', 'treatment', 'csd', 'M', 'dec', 'inc'] for line in data: PmagRec = {} rec = line.replace('\n', '').split() for k in range(len(keys)): PmagRec[keys[k]] = rec[k] PmagRecs.append(PmagRec) specs = pmag.get_dictkey(PmagRecs, 'specimen', '') sids = [] for spec in specs: if spec not in sids: sids.append(spec) # get list of unique specimen names for spc in sids: # step through the specimen names print(spc) specdata = pmag.get_dictitem(PmagRecs, 'specimen', spc, 'T') # get all this one's data DIMs, Temps = [], [] for dat in specdata: # step through the data DIMs.append( [float(dat['dec']), float(dat['inc']), float(dat['M']) * 1e-3]) Temps.append(float(dat['treatment'])) carts = pmag.dir2cart(DIMs).transpose() # if norm==1: # want to normalize # nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values # ylab="M/M_max" if norm == 1: # want to normalize nrm = (DIMs[0][2]) # normalize by NRM ylab = "M/M_o" else: nrm = 1. # don't normalize ylab = "Magnetic moment (Am^2)" xlab = "Temperature (C)" pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(abs(carts[0]), nrm), sym='r-') pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(abs(carts[0]), nrm), sym='ro') # X direction pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(abs(carts[1]), nrm), sym='c-') pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(abs(carts[1]), nrm), sym='cs') # Y direction pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(abs(carts[2]), nrm), sym='k-') pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(abs(carts[2]), nrm), sym='k^', title=spc, xlab=xlab, ylab=ylab) # Z direction files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt} if plot == 0: pmagplotlib.drawFIGS(FIG) ans = input('S[a]ve figure? [q]uit, <return> to continue ') if ans == 'a': pmagplotlib.saveP(FIG, files) elif ans == 'q': sys.exit() else: pmagplotlib.saveP(FIG, files) pmagplotlib.clearFIG(FIG['lowrie'])
def test_open_file_unicode(self): fname = os.path.join(WD, 'data_files', '3_0', 'Megiddo', 'sites.txt') data = pmag.open_file(fname) print(len(data)) self.assertEqual(len(data), 41)
def convert(**kwargs): # initialize some stuff methcode="LP-NO" phi,theta,peakfield,labfield=0,0,0,0 pTRM,MD=0,0 dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0] inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45] tdec=[0,90,0,180,270,0,0,90,0] tinc=[0,0,90,0,0,-90,0,0,90] missing=1 demag="N" citations='This study' fmt='old' Samps=[] trm=0 irm=0 #get args user = kwargs.get('user', '') dir_path = kwargs.get('dir_path', '.') output_dir_path = dir_path meas_file = kwargs.get('meas_file', 'measurements.txt') spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile site_file = kwargs.get('site_file', 'sites.txt') # site outfile loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile mag_file = kwargs.get('mag_file', '') labfield = kwargs.get('labfield', '') if labfield: labfield = float(labfield) *1e-6 else: labfield = 0 phi = kwargs.get('phi', 0) if phi: phi = float(phi) else: phi = 0 theta = kwargs.get('theta', 0) if theta: theta=float(theta) else: theta = 0 peakfield = kwargs.get('peakfield', 0) if peakfield: peakfield=float(peakfield) *1e-3 else: peakfield = 0 specnum = kwargs.get('specnum', 0) samp_con = kwargs.get('samp_con', '1') location = kwargs.get('location', 'unknown') samp_infile = kwargs.get('samp_infile', '') syn = kwargs.get('syn', 0) institution = kwargs.get('institution', '') syntype = kwargs.get('syntype', '') inst = kwargs.get('inst', '') noave = kwargs.get('noave', 0) codelist = kwargs.get('codelist', '') coil = kwargs.get('coil', '') cooling_rates = kwargs.get('cooling_rates', '') lat = kwargs.get('lat', '') lon = kwargs.get('lon', '') timezone = kwargs.get('timezone', 'UTC') # make sure all initial values are correctly set up (whether they come from the command line or a GUI) if samp_infile: Samps, file_type = pmag.magic_read(samp_infile) if coil: coil = str(coil) methcode="LP-IRM" irmunits = "V" if coil not in ["1","2","3"]: print(__doc__) print('not a valid coil specification') return False, '{} is not a valid coil specification'.format(coil) if mag_file: lines = pmag.open_file(mag_file) if not lines: print("you must provide a valid mag_file") return False, "you must provide a valid mag_file" if not mag_file: print(__doc__) print("mag_file field is required option") return False, "mag_file field is required option" if specnum!=0: specnum=-specnum if "4" == samp_con[0]: if "-" not in samp_con: print("naming convention option [4] must be in form 4-Z where Z is an integer") print('---------------') return False, "naming convention option [4] must be in form 4-Z where Z is an integer" else: Z=samp_con.split("-")[1] samp_con="4" if "7" == samp_con[0]: if "-" not in samp_con: print("option [7] must be in form 7-Z where Z is an integer") return False, "option [7] must be in form 7-Z where Z is an integer" else: Z=samp_con.split("-")[1] samp_con="7" else: Z = 0 if codelist: codes=codelist.split(':') if "AF" in codes: demag='AF' if'-dc' not in sys.argv: methcode="LT-AF-Z" if'-dc' in sys.argv: methcode="LT-AF-I" if "T" in codes: demag="T" if '-dc' not in sys.argv: methcode="LT-T-Z" if '-dc' in sys.argv: methcode="LT-T-I" if "I" in codes: methcode="LP-IRM" irmunits="mT" if "I3d" in codes: methcode="LT-T-Z:LP-IRM-3D" if "S" in codes: demag="S" methcode="LP-PI-TRM:LP-PI-ALT-AFARM" trm_labfield=labfield ans=input("DC lab field for ARM step: [50uT] ") if ans=="": arm_labfield=50e-6 else: arm_labfield=float(ans)*1e-6 ans=input("temperature for total trm step: [600 C] ") if ans=="": trm_peakT=600+273 # convert to kelvin else: trm_peakT=float(ans)+273 # convert to kelvin if "G" in codes: methcode="LT-AF-G" if "D" in codes: methcode="LT-AF-D" if "TRM" in codes: demag="T" trm=1 if "CR" in codes: demag="T" cooling_rate_experiment=1 if command_line: ind=sys.argv.index("CR") cooling_rates=sys.argv[ind+1] cooling_rates_list=cooling_rates.split(',') else: cooling_rates_list=str(cooling_rates).split(',') if demag=="T" and "ANI" in codes: methcode="LP-AN-TRM" if demag=="T" and "CR" in codes: methcode="LP-CR-TRM" if demag=="AF" and "ANI" in codes: methcode="LP-AN-ARM" if labfield==0: labfield=50e-6 if peakfield==0: peakfield=.180 MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[] version_num=pmag.get_version() ################################## for line in lines: instcode="" if len(line)>2: MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{} MeasRec['software_packages']=version_num MeasRec["description"]="" MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin MeasRec["treat_ac_field"]='0' MeasRec["treat_dc_field"]='0' MeasRec["treat_dc_field_phi"]='0' MeasRec["treat_dc_field_theta"]='0' meas_type="LT-NO" rec=line.split() try: float(rec[0]); print("No specimen name for line #%d in the measurement file"%lines.index(line)); continue except ValueError: pass if rec[1]==".00":rec[1]="0.00" treat=rec[1].split('.') if methcode=="LP-IRM": if irmunits=='mT': labfield=float(treat[0])*1e-3 else: labfield=pmag.getfield(irmunits,coil,treat[0]) if rec[1][0]!="-": phi,theta=0.,90. else: phi,theta=0.,-90. meas_type="LT-IRM" MeasRec["treat_dc_field"]='%8.3e'%(labfield) MeasRec["treat_dc_field_phi"]='%7.1f'%(phi) MeasRec["treat_dc_field_theta"]='%7.1f'%(theta) if len(rec)>6: code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time if len(code1)==2: # old format with AM/PM missing=0 code2=code1[0].split('/') # break date into mon/day/year code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements yy=int(code2[2]) if yy <90: yyyy=str(2000+yy) else: yyyy=str(1900+yy) mm=int(code2[0]) if mm<10: mm="0"+str(mm) else: mm=str(mm) dd=int(code2[1]) if dd<10: dd="0"+str(dd) else: dd=str(dd) time=code1[1].split(':') hh=int(time[0]) if code3[0]=="PM":hh=hh+12 if hh<10: hh="0"+str(hh) else: hh=str(hh) min=int(time[1]) if min<10: min= "0"+str(min) else: min=str(min) dt=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00" local = pytz.timezone(timezone) naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S") local_dt = local.localize(naive, is_dst=None) utc_dt = local_dt.astimezone(pytz.utc) MeasRec["timestamp"]=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z" if inst=="": if code3[1][0]=='C':instcode='SIO-bubba' if code3[1][0]=='G':instcode='SIO-flo' else: instcode='' MeasRec["meas_n_orient"]=code3[1][2] elif len(code1)>2: # newest format (cryo7 or later) if "LP-AN-ARM" not in methcode:labfield=0 fmt='new' date=code1[0].split('/') # break date into mon/day/year yy=int(date[2]) if yy <90: yyyy=str(2000+yy) else: yyyy=str(1900+yy) mm=int(date[0]) if mm<10: mm="0"+str(mm) else: mm=str(mm) dd=int(date[1]) if dd<10: dd="0"+str(dd) else: dd=str(dd) time=code1[1].split(':') hh=int(time[0]) if hh<10: hh="0"+str(hh) else: hh=str(hh) min=int(time[1]) if min<10: min= "0"+str(min) else: min=str(min) dt=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00" local = pytz.timezone(timezone) naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S") local_dt = local.localize(naive, is_dst=None) utc_dt = local_dt.astimezone(pytz.utc) MeasRec["timestamp"]=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z" if inst=="": if code1[6][0]=='C': instcode='SIO-bubba' if code1[6][0]=='G': instcode='SIO-flo' else: instcode='' if len(code1)>1: MeasRec["meas_n_orient"]=code1[6][2] else: MeasRec["meas_n_orient"]=code1[7] # takes care of awkward format with bubba and flo being different if user=="":user=code1[5] if code1[2][-1]=='C': demag="T" if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6 if code1[2]=='mT' and methcode!="LP-IRM": demag="AF" if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6 if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM": phi,theta=0.,-90. if demag=="T": meas_type="LT-T-I" if demag=="AF": meas_type="LT-AF-I" MeasRec["treat_dc_field"]='%8.3e'%(labfield) MeasRec["treat_dc_field_phi"]='%7.1f'%(phi) MeasRec["treat_dc_field_theta"]='%7.1f'%(theta) if code1[4]=='' or labfield==0. and meas_type!="LT-IRM": if demag=='T':meas_type="LT-T-Z" if demag=="AF":meas_type="LT-AF-Z" MeasRec["treat_dc_field"]='0' if syn==0: specimen=rec[0] MeasRec["specimen"]=specimen if specnum!=0: sample=rec[0][:specnum] else: sample=rec[0] if samp_infile and Samps: # if samp_infile was provided AND yielded sample data samp=pmag.get_dictitem(Samps,'sample',sample,'T') if len(samp)>0: location=samp[0]["location"] site=samp[0]["site"] else: location='' site='' else: site=pmag.parse_site(sample,samp_con,Z) if location!='' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]: LocRec['location'] = location LocRec['lat_n'] = lat LocRec['lat_s'] = lat LocRec['lon_e'] = lon LocRec['lon_w'] = lon LocRecs.append(LocRec) if site!='' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]: SiteRec['location'] = location SiteRec['site'] = site SiteRec['lat'] = lat SiteRec['lon'] = lon SiteRecs.append(SiteRec) if sample!='' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]: SampRec['site'] = site SampRec['sample'] = sample SampRecs.append(SampRec) if specimen!='' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]: SpecRec["specimen"]=specimen SpecRec['sample'] = sample SpecRecs.append(SpecRec) else: specimen=rec[0] MeasRec["specimen"]=specimen if specnum!=0: sample=rec[0][:specnum] else: sample=rec[0] site=pmag.parse_site(sample,samp_con,Z) if location!='' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]: LocRec['location'] = location LocRec['lat_n'] = lat LocRec['lat_s'] = lat LocRec['lon_e'] = lon LocRec['lon_w'] = lon LocRecs.append(LocRec) if site!='' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]: SiteRec['location'] = location SiteRec['site'] = site SiteRec['lat'] = lat SiteRec['lon'] = lon SiteRecs.append(SiteRec) if sample!='' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]: SampRec['site'] = site SampRec['sample'] = sample SampRecs.append(SampRec) if specimen!='' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]: SpecRec["specimen"]=specimen SpecRec['sample'] = sample SpecRecs.append(SpecRec) SampRec["institution"]=institution SampRec["material_type"]=syntype if float(rec[1])==0: pass elif demag=="AF": if methcode != "LP-AN-ARM": MeasRec["treat_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla if meas_type=="LT-AF-Z": MeasRec["treat_dc_field"]='0' else: # AARM experiment if treat[1][0]=='0': meas_type="LT-AF-Z:LP-AN-ARM:" MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla MeasRec["treat_dc_field"]='%8.3e'%(0) if labfield!=0 and methcode!="LP-AN-ARM": print("Warning - inconsistency in mag file with lab field - overriding file with 0") else: meas_type="LT-AF-I:LP-AN-ARM" ipos=int(treat[0])-1 MeasRec["treat_dc_field_phi"]='%7.1f' %(dec[ipos]) MeasRec["treat_dc_field_theta"]='%7.1f'% (inc[ipos]) MeasRec["treat_dc_field"]='%8.3e'%(labfield) MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla elif demag=="T" and methcode == "LP-AN-TRM": MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin if treat[1][0]=='0': meas_type="LT-T-Z:LP-AN-TRM" MeasRec["treat_dc_field"]='%8.3e'%(0) MeasRec["treat_dc_field_phi"]='0' MeasRec["treat_dc_field_theta"]='0' else: MeasRec["treat_dc_field"]='%8.3e'%(labfield) if treat[1][0]=='7': # alteration check as final measurement meas_type="LT-PTRM-I:LP-AN-TRM" else: meas_type="LT-T-I:LP-AN-TRM" # find the direction of the lab field in two ways: # (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z) ipos_code=int(treat[1][0])-1 # (2) using the magnetization DEC=float(rec[4]) INC=float(rec[5]) if INC < 45 and INC > -45: if DEC>315 or DEC<45: ipos_guess=0 if DEC>45 and DEC<135: ipos_guess=1 if DEC>135 and DEC<225: ipos_guess=3 if DEC>225 and DEC<315: ipos_guess=4 else: if INC >45: ipos_guess=2 if INC <-45: ipos_guess=5 # prefer the guess over the code ipos=ipos_guess MeasRec["treat_dc_field_phi"]='%7.1f' %(tdec[ipos]) MeasRec["treat_dc_field_theta"]='%7.1f'% (tinc[ipos]) # check it if ipos_guess!=ipos_code and treat[1][0]!='7': print("-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat)))) elif demag=="S": # Shaw experiment if treat[1][1]=='0': if int(treat[0])!=0: MeasRec["treat_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla MeasRec["treat_dc_field"]='0' meas_type="LT-AF-Z" # first AF else: meas_type="LT-NO" MeasRec["treat_ac_field"]='0' MeasRec["treat_dc_field"]='0' elif treat[1][1]=='1': if int(treat[0])==0: MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla MeasRec["treat_dc_field"]='%8.3e'%(arm_labfield) MeasRec["treat_dc_field_phi"]='%7.1f'%(phi) MeasRec["treat_dc_field_theta"]='%7.1f'%(theta) meas_type="LT-AF-I" else: MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla MeasRec["treat_dc_field"]='0' meas_type="LT-AF-Z" elif treat[1][1]=='2': if int(treat[0])==0: MeasRec["treat_ac_field"]='0' MeasRec["treat_dc_field"]='%8.3e'%(trm_labfield) MeasRec["treat_dc_field_phi"]='%7.1f'%(phi) MeasRec["treat_dc_field_theta"]='%7.1f'%(theta) MeasRec["treat_temp"]='%8.3e' % (trm_peakT) meas_type="LT-T-I" else: MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla MeasRec["treat_dc_field"]='0' meas_type="LT-AF-Z" elif treat[1][1]=='3': if int(treat[0])==0: MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla MeasRec["treat_dc_field"]='%8.3e'%(arm_labfield) MeasRec["treat_dc_field_phi"]='%7.1f'%(phi) MeasRec["treat_dc_field_theta"]='%7.1f'%(theta) meas_type="LT-AF-I" else: MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla MeasRec["treat_dc_field"]='0' meas_type="LT-AF-Z" # Cooling rate experient # added by rshaar elif demag=="T" and methcode == "LP-CR-TRM": MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin if treat[1][0]=='0': meas_type="LT-T-Z:LP-CR-TRM" MeasRec["treat_dc_field"]='%8.3e'%(0) MeasRec["treat_dc_field_phi"]='0' MeasRec["treat_dc_field_theta"]='0' else: MeasRec["treat_dc_field"]='%8.3e'%(labfield) if treat[1][0]=='7': # alteration check as final measurement meas_type="LT-PTRM-I:LP-CR-TRM" else: meas_type="LT-T-I:LP-CR-TRM" MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta indx=int(treat[1][0])-1 # alteration check matjed as 0.7 in the measurement file if indx==6: cooling_time= cooling_rates_list[-1] else: cooling_time=cooling_rates_list[indx] MeasRec["description"]="cooling_rate"+":"+cooling_time+":"+"K/min" elif demag!='N': if len(treat)==1:treat.append('0') MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin if trm==0: # demag=T and not trmaq if treat[1][0]=='0': meas_type="LT-T-Z" else: MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT) MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step if treat[1][0]=='2': meas_type="LT-PTRM-I" # pTRM check pTRM=1 if treat[1][0]=='3': MeasRec["treat_dc_field"]='0' # this is a zero field step meas_type="LT-PTRM-MD" # pTRM tail check else: labfield=float(treat[1])*1e-6 MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT) MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta meas_type="LT-T-I:LP-TRM" # trm acquisition experiment MeasRec["dir_csd"]=rec[2] MeasRec["magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu) MeasRec["dir_dec"]=rec[4] MeasRec["dir_inc"]=rec[5] MeasRec["instrument_codes"]=instcode MeasRec["analysts"]=user MeasRec["citations"]=citations if "LP-IRM-3D" in methcode : meas_type=methcode #MeasRec["method_codes"]=methcode.strip(':') MeasRec["method_codes"]=meas_type MeasRec["quality"]='g' if 'std' in rec[0]: MeasRec["standard"]='s' else: MeasRec["standard"]='u' MeasRec["treat_step_num"]='1' #print MeasRec['treat_temp'] MeasRecs.append(MeasRec) con = nb.Contribution(output_dir_path,read_tables=[]) # create MagIC tables con.add_magic_table_from_data(dtype='specimens', data=SpecRecs) con.add_magic_table_from_data(dtype='samples', data=SampRecs) con.add_magic_table_from_data(dtype='sites', data=SiteRecs) con.add_magic_table_from_data(dtype='locations', data=LocRecs) MeasOuts=pmag.measurements_methods3(MeasRecs,noave) con.add_magic_table_from_data(dtype='measurements', data=MeasOuts) # write MagIC tables to file con.tables['specimens'].write_magic_file(custom_name=spec_file) con.tables['samples'].write_magic_file(custom_name=samp_file) con.tables['sites'].write_magic_file(custom_name=site_file) con.tables['locations'].write_magic_file(custom_name=loc_file) con.tables['measurements'].write_magic_file(custom_name=meas_file) return True, meas_file
def test_open_file_unicode(self): fname = os.path.join(WD, 'data_files', '3_0', 'Megiddo', 'sites.txt') data = pmag.open_file(fname) print(len(data)) self.assertEqual(len(data), 41)
def test_open_file_non_unicode(self): fname = os.path.join(WD, 'data_files', 'lowrie', 'lowrie_example.dat') data = pmag.open_file(fname) self.assertTrue(len(data) >= 465)
def test_open_file_non_unicode(self): fname = os.path.join(WD, 'data_files', 'lowrie', 'lowrie_example.dat') data = pmag.open_file(fname) self.assertTrue(len(data) >= 465)
def main(command_line=True, **kwargs): """ NAME sio_magic.py DESCRIPTION converts SIO .mag format files to magic_measurements format files SYNTAX sio_magic.py [command line options] OPTIONS -h: prints the help message and quits. -usr USER: identify user, default is "" -f FILE: specify .mag format input file, required -fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none -- values in SAMPFILE will override selections for -loc (location), -spc (designate specimen), and -ncn (sample-site naming convention) -F FILE: specify output file, default is magic_measurements.txt -Fsy: specify er_synthetics file, default is er_sythetics.txt -LP [colon delimited list of protocols, include all that apply] AF: af demag T: thermal including thellier but not trm acquisition S: Shaw method I: IRM (acquisition) I3d: 3D IRM experiment N: NRM only TRM: trm acquisition ANI: anisotropy experiment D: double AF demag G: triple AF demag (GRM protocol) CR: cooling rate experiment. The treatment coding of the measurement file should be: XXX.00,XXX.10, XXX.20 ...XX.70 etc. (XXX.00 is optional) where XXX in the temperature and .10,.20... are running numbers of the cooling rates steps. XXX.00 is optional zerofield baseline. XXX.70 is alteration check. syntax in sio_magic is: -LP CR xxx,yyy,zzz,..... xxx -A where xxx, yyy, zzz...xxx are cooling time in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70 if you use a zerofield step then no need to specify the cooling rate for the zerofield It is important to add to the command line the -A option so the measurements will not be averaged. But users need to make sure that there are no duplicate measurements in the file -V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3 -spc NUM : specify number of characters to designate a specimen, default = 0 -loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic -syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE -ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is "" -dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment -ac B : peak AF field (in mT) for ARM acquisition, default is none -ncn NCON: specify naming convention: default is #1 below -A: don't average replicate measurements Sample naming convention: [1] XXXXY: where XXXX is an arbitrary length site designation and Y is the single character sample designation. e.g., TG001a is the first sample from site TG001. [default] [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length) [4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX [5] site name same as sample [6] site is entered under a separate column NOT CURRENTLY SUPPORTED [7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY NB: all others you will have to customize your self or e-mail [email protected] for help. [8] synthetic - has no site name [9] ODP naming convention INPUT Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in seperate .mag files (eg. af.mag, thermal.mag, etc.) Format of SIO .mag files: Spec Treat CSD Intensity Declination Inclination [optional metadata string] Spec: specimen name Treat: treatment step XXX T in Centigrade XXX AF in mT for special experiments: Thellier: XXX.0 first zero field step XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order] XXX.2 second in-field step at lower temperature (pTRM check) XXX.3 second zero-field step after infield (pTRM check step) XXX.3 MUST be done in this order [XXX.0, XXX.1 [optional XXX.2] XXX.3] AARM: X.00 baseline step (AF in zero bias field - high peak field) X.1 ARM step (in field step) where X is the step number in the 15 position scheme (see Appendix to Lecture 13 - http://magician.ucsd.edu/Essentials_2) ATRM: X.00 optional baseline X.1 ATRM step (+X) X.2 ATRM step (+Y) X.3 ATRM step (+Z) X.4 ATRM step (-X) X.5 ATRM step (-Y) X.6 ATRM step (-Z) X.7 optional alteration check (+X) TRM: XXX.YYY XXX is temperature step of total TRM YYY is dc field in microtesla Intensity assumed to be total moment in 10^3 Am^2 (emu) Declination: Declination in specimen coordinate system Inclination: Declination in specimen coordinate system Optional metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS hh in 24 hours. dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively xx.xxx DC field UNITS of DC field (microT, mT) INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes, measured in four positions) NMEAS: number of measurements in a single position (1,3,200...) """ # initialize some stuff mag_file = None codelist = None infile_type="mag" noave=0 methcode,inst="LP-NO","" phi,theta,peakfield,labfield=0,0,0,0 pTRM,MD,samp_con,Z=0,0,'1',1 dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0] inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45] tdec=[0,90,0,180,270,0,0,90,0] tinc=[0,0,90,0,0,-90,0,0,90] missing=1 demag="N" er_location_name="" citation='This study' args=sys.argv fmt='old' syn=0 synfile='er_synthetics.txt' samp_infile,Samps='',[] trm=0 irm=0 specnum=0 coil="" mag_file="" # # get command line arguments # meas_file="magic_measurements.txt" user="" if not command_line: user = kwargs.get('user', '') meas_file = kwargs.get('meas_file', '') syn_file = kwargs.get('syn_file', '') mag_file = kwargs.get('mag_file', '') labfield = kwargs.get('labfield', '') if labfield: labfield = float(labfield) *1e-6 else: labfield = 0 phi = kwargs.get('phi', 0) if phi: phi = float(phi) else: phi = 0 theta = kwargs.get('theta', 0) if theta: theta=float(theta) else: theta = 0 peakfield = kwargs.get('peakfield', 0) if peakfield: peakfield=float(peakfield) *1e-3 else: peakfield = 0 specnum = kwargs.get('specnum', 0) samp_con = kwargs.get('samp_con', '1') er_location_name = kwargs.get('er_location_name', '') samp_infile = kwargs.get('samp_infile', '') syn = kwargs.get('syn', 0) institution = kwargs.get('institution', '') syntype = kwargs.get('syntype', '') inst = kwargs.get('inst', '') noave = kwargs.get('noave', 0) codelist = kwargs.get('codelist', '') coil = kwargs.get('coil', '') cooling_rates = kwargs.get('cooling_rates', '') if command_line: if "-h" in args: print(main.__doc__) return False if "-usr" in args: ind=args.index("-usr") user=args[ind+1] if '-F' in args: ind=args.index("-F") meas_file=args[ind+1] if '-Fsy' in args: ind=args.index("-Fsy") synfile=args[ind+1] if '-f' in args: ind=args.index("-f") mag_file=args[ind+1] if "-dc" in args: ind=args.index("-dc") labfield=float(args[ind+1])*1e-6 phi=float(args[ind+2]) theta=float(args[ind+3]) if "-ac" in args: ind=args.index("-ac") peakfield=float(args[ind+1])*1e-3 if "-spc" in args: ind=args.index("-spc") specnum=int(args[ind+1]) if "-loc" in args: ind=args.index("-loc") er_location_name=args[ind+1] if "-fsa" in args: ind=args.index("-fsa") samp_infile = args[ind+1] if '-syn' in args: syn=1 ind=args.index("-syn") institution=args[ind+1] syntype=args[ind+2] if '-fsy' in args: ind=args.index("-fsy") synfile=args[ind+1] if "-ins" in args: ind=args.index("-ins") inst=args[ind+1] if "-A" in args: noave=1 if "-ncn" in args: ind=args.index("-ncn") samp_con=sys.argv[ind+1] if '-LP' in args: ind=args.index("-LP") codelist=args[ind+1] if "-V" in args: ind=args.index("-V") coil=args[ind+1] # make sure all initial values are correctly set up (whether they come from the command line or a GUI) if samp_infile: Samps, file_type = pmag.magic_read(samp_infile) if coil: coil = str(coil) methcode="LP-IRM" irmunits = "V" if coil not in ["1","2","3"]: print(main.__doc__) print('not a valid coil specification') return False, '{} is not a valid coil specification'.format(coil) if mag_file: try: #with open(mag_file,'r') as finput: # lines = finput.readlines() lines=pmag.open_file(mag_file) except: print("bad mag file name") return False, "bad mag file name" if not mag_file: print(main.__doc__) print("mag_file field is required option") return False, "mag_file field is required option" if specnum!=0: specnum=-specnum #print 'samp_con:', samp_con if samp_con: if "4" == samp_con[0]: if "-" not in samp_con: print("naming convention option [4] must be in form 4-Z where Z is an integer") print('---------------') return False, "naming convention option [4] must be in form 4-Z where Z is an integer" else: Z=samp_con.split("-")[1] samp_con="4" if "7" == samp_con[0]: if "-" not in samp_con: print("option [7] must be in form 7-Z where Z is an integer") return False, "option [7] must be in form 7-Z where Z is an integer" else: Z=samp_con.split("-")[1] samp_con="7" if codelist: codes=codelist.split(':') if "AF" in codes: demag='AF' if'-dc' not in args: methcode="LT-AF-Z" if'-dc' in args: methcode="LT-AF-I" if "T" in codes: demag="T" if '-dc' not in args: methcode="LT-T-Z" if '-dc' in args: methcode="LT-T-I" if "I" in codes: methcode="LP-IRM" irmunits="mT" if "I3d" in codes: methcode="LT-T-Z:LP-IRM-3D" if "S" in codes: demag="S" methcode="LP-PI-TRM:LP-PI-ALT-AFARM" trm_labfield=labfield ans=input("DC lab field for ARM step: [50uT] ") if ans=="": arm_labfield=50e-6 else: arm_labfield=float(ans)*1e-6 ans=input("temperature for total trm step: [600 C] ") if ans=="": trm_peakT=600+273 # convert to kelvin else: trm_peakT=float(ans)+273 # convert to kelvin if "G" in codes: methcode="LT-AF-G" if "D" in codes: methcode="LT-AF-D" if "TRM" in codes: demag="T" trm=1 if "CR" in codes: demag="T" cooling_rate_experiment=1 if command_line: ind=args.index("CR") cooling_rates=args[ind+1] cooling_rates_list=cooling_rates.split(',') else: cooling_rates_list=str(cooling_rates).split(',') if demag=="T" and "ANI" in codes: methcode="LP-AN-TRM" if demag=="T" and "CR" in codes: methcode="LP-CR-TRM" if demag=="AF" and "ANI" in codes: methcode="LP-AN-ARM" if labfield==0: labfield=50e-6 if peakfield==0: peakfield=.180 SynRecs,MagRecs=[],[] version_num=pmag.get_version() ################################## if 1: #if infile_type=="SIO format": for line in lines: instcode="" if len(line)>2: SynRec={} MagRec={} MagRec['er_location_name']=er_location_name MagRec['magic_software_packages']=version_num MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["treatment_ac_field"]='0' MagRec["treatment_dc_field"]='0' MagRec["treatment_dc_field_phi"]='0' MagRec["treatment_dc_field_theta"]='0' meas_type="LT-NO" rec=line.split() if rec[1]==".00":rec[1]="0.00" treat=rec[1].split('.') if methcode=="LP-IRM": if irmunits=='mT': labfield=float(treat[0])*1e-3 else: labfield=pmag.getfield(irmunits,coil,treat[0]) if rec[1][0]!="-": phi,theta=0.,90. else: phi,theta=0.,-90. meas_type="LT-IRM" MagRec["treatment_dc_field"]='%8.3e'%(labfield) MagRec["treatment_dc_field_phi"]='%7.1f'%(phi) MagRec["treatment_dc_field_theta"]='%7.1f'%(theta) if len(rec)>6: code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time if len(code1)==2: # old format with AM/PM missing=0 code2=code1[0].split('/') # break date into mon/day/year code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements yy=int(code2[2]) if yy <90: yyyy=str(2000+yy) else: yyyy=str(1900+yy) mm=int(code2[0]) if mm<10: mm="0"+str(mm) else: mm=str(mm) dd=int(code2[1]) if dd<10: dd="0"+str(dd) else: dd=str(dd) time=code1[1].split(':') hh=int(time[0]) if code3[0]=="PM":hh=hh+12 if hh<10: hh="0"+str(hh) else: hh=str(hh) min=int(time[1]) if min<10: min= "0"+str(min) else: min=str(min) MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00" MagRec["measurement_time_zone"]='SAN' if inst=="": if code3[1][0]=='C':instcode='SIO-bubba' if code3[1][0]=='G':instcode='SIO-flo' else: instcode='' MagRec["measurement_positions"]=code3[1][2] elif len(code1)>2: # newest format (cryo7 or later) if "LP-AN-ARM" not in methcode:labfield=0 fmt='new' date=code1[0].split('/') # break date into mon/day/year yy=int(date[2]) if yy <90: yyyy=str(2000+yy) else: yyyy=str(1900+yy) mm=int(date[0]) if mm<10: mm="0"+str(mm) else: mm=str(mm) dd=int(date[1]) if dd<10: dd="0"+str(dd) else: dd=str(dd) time=code1[1].split(':') hh=int(time[0]) if hh<10: hh="0"+str(hh) else: hh=str(hh) min=int(time[1]) if min<10: min= "0"+str(min) else: min=str(min) MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00" MagRec["measurement_time_zone"]='SAN' if inst=="": if code1[6][0]=='C': instcode='SIO-bubba' if code1[6][0]=='G': instcode='SIO-flo' else: instcode='' if len(code1)>1: MagRec["measurement_positions"]=code1[6][2] else: MagRec["measurement_positions"]=code1[7] # takes care of awkward format with bubba and flo being different if user=="":user=code1[5] if code1[2][-1]=='C': demag="T" if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6 if code1[2]=='mT' and methcode!="LP-IRM": demag="AF" if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6 if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM": phi,theta=0.,-90. if demag=="T": meas_type="LT-T-I" if demag=="AF": meas_type="LT-AF-I" MagRec["treatment_dc_field"]='%8.3e'%(labfield) MagRec["treatment_dc_field_phi"]='%7.1f'%(phi) MagRec["treatment_dc_field_theta"]='%7.1f'%(theta) if code1[4]=='' or labfield==0. and meas_type!="LT-IRM": if demag=='T':meas_type="LT-T-Z" if demag=="AF":meas_type="LT-AF-Z" MagRec["treatment_dc_field"]='0' if syn==0: MagRec["er_specimen_name"]=rec[0] MagRec["er_synthetic_name"]="" MagRec["er_site_name"]="" if specnum!=0: MagRec["er_sample_name"]=rec[0][:specnum] else: MagRec["er_sample_name"]=rec[0] if samp_infile and Samps: # if samp_infile was provided AND yielded sample data samp=pmag.get_dictitem(Samps,'er_sample_name',MagRec['er_sample_name'],'T') if len(samp)>0: MagRec["er_location_name"]=samp[0]["er_location_name"] MagRec["er_site_name"]=samp[0]["er_site_name"] else: MagRec['er_location_name']='' MagRec["er_site_name"]='' elif int(samp_con)!=6: site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z) MagRec["er_site_name"]=site if MagRec['er_site_name']=="": print('No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']) if MagRec["er_location_name"]=="": print('no location name for: ',MagRec["er_specimen_name"]) else: MagRec["er_specimen_name"]=rec[0] if specnum!=0: MagRec["er_sample_name"]=rec[0][:specnum] else: MagRec["er_sample_name"]=rec[0] MagRec["er_site_name"]="" MagRec["er_synthetic_name"]=MagRec["er_specimen_name"] SynRec["er_synthetic_name"]=MagRec["er_specimen_name"] site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z) SynRec["synthetic_parent_sample"]=site SynRec["er_citation_names"]="This study" SynRec["synthetic_institution"]=institution SynRec["synthetic_type"]=syntype SynRecs.append(SynRec) if float(rec[1])==0: pass elif demag=="AF": if methcode != "LP-AN-ARM": MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla if meas_type=="LT-AF-Z": MagRec["treatment_dc_field"]='0' else: # AARM experiment if treat[1][0]=='0': meas_type="LT-AF-Z:LP-AN-ARM:" MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla MagRec["treatment_dc_field"]='%8.3e'%(0) if labfield!=0 and methcode!="LP-AN-ARM": print("Warning - inconsistency in mag file with lab field - overriding file with 0") else: meas_type="LT-AF-I:LP-AN-ARM" ipos=int(treat[0])-1 MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos]) MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos]) MagRec["treatment_dc_field"]='%8.3e'%(labfield) MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla elif demag=="T" and methcode == "LP-AN-TRM": MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin if treat[1][0]=='0': meas_type="LT-T-Z:LP-AN-TRM" MagRec["treatment_dc_field"]='%8.3e'%(0) MagRec["treatment_dc_field_phi"]='0' MagRec["treatment_dc_field_theta"]='0' else: MagRec["treatment_dc_field"]='%8.3e'%(labfield) if treat[1][0]=='7': # alteration check as final measurement meas_type="LT-PTRM-I:LP-AN-TRM" else: meas_type="LT-T-I:LP-AN-TRM" # find the direction of the lab field in two ways: # (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z) ipos_code=int(treat[1][0])-1 # (2) using the magnetization DEC=float(rec[4]) INC=float(rec[5]) if INC < 45 and INC > -45: if DEC>315 or DEC<45: ipos_guess=0 if DEC>45 and DEC<135: ipos_guess=1 if DEC>135 and DEC<225: ipos_guess=3 if DEC>225 and DEC<315: ipos_guess=4 else: if INC >45: ipos_guess=2 if INC <-45: ipos_guess=5 # prefer the guess over the code ipos=ipos_guess MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec[ipos]) MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc[ipos]) # check it if ipos_guess!=ipos_code and treat[1][0]!='7': print("-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat)))) elif demag=="S": # Shaw experiment if treat[1][1]=='0': if int(treat[0])!=0: MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla MagRec["treatment_dc_field"]='0' meas_type="LT-AF-Z" # first AF else: meas_type="LT-NO" MagRec["treatment_ac_field"]='0' MagRec["treatment_dc_field"]='0' elif treat[1][1]=='1': if int(treat[0])==0: MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield) MagRec["treatment_dc_field_phi"]='%7.1f'%(phi) MagRec["treatment_dc_field_theta"]='%7.1f'%(theta) meas_type="LT-AF-I" else: MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla MagRec["treatment_dc_field"]='0' meas_type="LT-AF-Z" elif treat[1][1]=='2': if int(treat[0])==0: MagRec["treatment_ac_field"]='0' MagRec["treatment_dc_field"]='%8.3e'%(trm_labfield) MagRec["treatment_dc_field_phi"]='%7.1f'%(phi) MagRec["treatment_dc_field_theta"]='%7.1f'%(theta) MagRec["treatment_temp"]='%8.3e' % (trm_peakT) meas_type="LT-T-I" else: MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla MagRec["treatment_dc_field"]='0' meas_type="LT-AF-Z" elif treat[1][1]=='3': if int(treat[0])==0: MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield) MagRec["treatment_dc_field_phi"]='%7.1f'%(phi) MagRec["treatment_dc_field_theta"]='%7.1f'%(theta) meas_type="LT-AF-I" else: MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla MagRec["treatment_dc_field"]='0' meas_type="LT-AF-Z" # Cooling rate experient # added by rshaar elif demag=="T" and methcode == "LP-CR-TRM": MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin if treat[1][0]=='0': meas_type="LT-T-Z:LP-CR-TRM" MagRec["treatment_dc_field"]='%8.3e'%(0) MagRec["treatment_dc_field_phi"]='0' MagRec["treatment_dc_field_theta"]='0' else: MagRec["treatment_dc_field"]='%8.3e'%(labfield) if treat[1][0]=='7': # alteration check as final measurement meas_type="LT-PTRM-I:LP-CR-TRM" else: meas_type="LT-T-I:LP-CR-TRM" MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta indx=int(treat[1][0])-1 # alteration check matjed as 0.7 in the measurement file if indx==6: cooling_time= cooling_rates_list[-1] else: cooling_time=cooling_rates_list[indx] MagRec["measurement_description"]="cooling_rate"+":"+cooling_time+":"+"K/min" elif demag!='N': if len(treat)==1:treat.append('0') MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin if trm==0: # demag=T and not trmaq if treat[1][0]=='0': meas_type="LT-T-Z" else: MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT) MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step if treat[1][0]=='2': meas_type="LT-PTRM-I" # pTRM check pTRM=1 if treat[1][0]=='3': MagRec["treatment_dc_field"]='0' # this is a zero field step meas_type="LT-PTRM-MD" # pTRM tail check else: labfield=float(treat[1])*1e-6 MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT) MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta meas_type="LT-T-I:LP-TRM" # trm acquisition experiment MagRec["measurement_csd"]=rec[2] MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu) MagRec["measurement_dec"]=rec[4] MagRec["measurement_inc"]=rec[5] MagRec["magic_instrument_codes"]=instcode MagRec["er_analyst_mail_names"]=user MagRec["er_citation_names"]=citation if "LP-IRM-3D" in methcode : meas_type=methcode #MagRec["magic_method_codes"]=methcode.strip(':') MagRec["magic_method_codes"]=meas_type MagRec["measurement_flag"]='g' MagRec["er_specimen_name"]=rec[0] if 'std' in rec[0]: MagRec["measurement_standard"]='s' else: MagRec["measurement_standard"]='u' MagRec["measurement_number"]='1' #print MagRec['treatment_temp'] MagRecs.append(MagRec) MagOuts=pmag.measurements_methods(MagRecs,noave) pmag.magic_write(meas_file,MagOuts,'magic_measurements') print("results put in ",meas_file) if len(SynRecs)>0: pmag.magic_write(synfile,SynRecs,'er_synthetics') print("synthetics put in ",synfile) return True, meas_file
def main(): """ NAME lowrie.py DESCRIPTION plots intensity decay curves for Lowrie experiments SYNTAX lowrie -h [command line options] INPUT takes SIO formatted input files OPTIONS -h prints help message and quits -f FILE: specify input file -N do not normalize by maximum magnetization -fmt [svg, pdf, eps, png] specify fmt, default is svg -sav save plots and quit """ fmt, plot = 'svg', 0 FIG = {} # plot dictionary FIG['lowrie'] = 1 # demag is figure 1 pmagplotlib.plot_init(FIG['lowrie'], 6, 6) norm = 1 # default is to normalize by maximum axis if len(sys.argv) > 1: if '-h' in sys.argv: print(main.__doc__) sys.exit() if '-N' in sys.argv: norm = 0 # don't normalize if '-sav' in sys.argv: plot = 1 # don't normalize if '-fmt' in sys.argv: # sets input filename ind = sys.argv.index("-fmt") fmt = sys.argv[ind + 1] if '-f' in sys.argv: # sets input filename ind = sys.argv.index("-f") in_file = sys.argv[ind + 1] else: print(main.__doc__) print('you must supply a file name') sys.exit() else: print(main.__doc__) print('you must supply a file name') sys.exit() data = pmag.open_file(in_file) PmagRecs = [] # set up a list for the results keys = ['specimen', 'treatment', 'csd', 'M', 'dec', 'inc'] for line in data: PmagRec = {} rec = line.replace('\n', '').split() for k in range(len(keys)): PmagRec[keys[k]] = rec[k] PmagRecs.append(PmagRec) specs = pmag.get_dictkey(PmagRecs, 'specimen', '') sids = [] for spec in specs: if spec not in sids: sids.append(spec) # get list of unique specimen names for spc in sids: # step through the specimen names print(spc) specdata = pmag.get_dictitem( PmagRecs, 'specimen', spc, 'T') # get all this one's data DIMs, Temps = [], [] for dat in specdata: # step through the data DIMs.append([float(dat['dec']), float( dat['inc']), float(dat['M']) * 1e-3]) Temps.append(float(dat['treatment'])) carts = pmag.dir2cart(DIMs).transpose() # if norm==1: # want to normalize # nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values # ylab="M/M_max" if norm == 1: # want to normalize nrm = (DIMs[0][2]) # normalize by NRM ylab = "M/M_o" else: nrm = 1. # don't normalize ylab = "Magnetic moment (Am^2)" xlab = "Temperature (C)" pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div( abs(carts[0]), nrm), sym='r-') pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div( abs(carts[0]), nrm), sym='ro') # X direction pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div( abs(carts[1]), nrm), sym='c-') pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div( abs(carts[1]), nrm), sym='cs') # Y direction pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div( abs(carts[2]), nrm), sym='k-') pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div( abs(carts[2]), nrm), sym='k^', title=spc, xlab=xlab, ylab=ylab) # Z direction files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt} if plot == 0: pmagplotlib.drawFIGS(FIG) ans = input('S[a]ve figure? [q]uit, <return> to continue ') if ans == 'a': pmagplotlib.saveP(FIG, files) elif ans == 'q': sys.exit() else: pmagplotlib.saveP(FIG, files) pmagplotlib.clearFIG(FIG['lowrie'])
def convert(**kwargs): version_num = pmag.get_version() dir_path = kwargs.get('dir_path', '.') mag_file = kwargs.get('mag_file') input_dir_path = kwargs.get('input_dir_path', dir_path) if input_dir_path == dir_path: mag_file = pmag.resolve_file_name(mag_file, dir_path) input_dir_path = os.path.split(mag_file)[0] output_dir_path = dir_path user = kwargs.get('user', '') meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile site_file = kwargs.get('site_file', 'sites.txt') # site outfile loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile specnum = kwargs.get('specnum', 1) samp_con = kwargs.get('samp_con', '1') location = kwargs.get('location', 'unknown') lat = kwargs.get('lat', '') lon = kwargs.get('lon', '') noave = kwargs.get('noave', 0) # default (0) means DO average meth_code = kwargs.get('meth_code', "LP-NO") volume = float(kwargs.get('volume', 2.5)) * 1e-6 timezone = kwargs.get('timestamp', 'UTC') # format variables mag_file = os.path.join(input_dir_path, mag_file) if specnum != 0: specnum = -int(specnum) if samp_con.startswith("4"): if "-" not in samp_con: print("option [4] must be in form 4-Z where Z is an integer") return False, "naming convention option [4] must be in form 4-Z where Z is an integer" else: Z = samp_con.split("-")[1] samp_con = "4" elif samp_con.startswith("7"): if "-" not in samp_con: print("option [7] must be in form 7-Z where Z is an integer") return False, "naming convention option [7] must be in form 7-Z where Z is an integer" else: Z = samp_con.split("-")[1] samp_con = "7" else: Z = 1 #create data holders MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], [] data = pmag.open_file(mag_file) # remove garbage/blank lines data = [i for i in data if len(i) >= 5] if not len(data): print('No data') return n = 0 end = False # loop through records while not end: first_line = data[n].split() sampleName = first_line[0] demagLevel = first_line[2] date = first_line[3] + ":0:0:0" n += 2 third_line = data[n].split() if not third_line[0].startswith('SPEC.ANGLES'): print('third line of a block should start with SPEC.ANGLES') print(third_line) return specimenAngleDec = third_line[1] specimenAngleInc = third_line[2] n += 4 while not data[n].startswith('MEAN'): n += 1 mean_line = data[n] Mx = mean_line[1] My = mean_line[2] Mz = mean_line[3] n += 1 precision_line = data[n].split() if not precision_line[0].startswith('Modulus'): print('precision line should start with "Modulus"') return splitExp = precision_line[2].split('A') intensityVolStr = precision_line[1] + splitExp[0] intensityVol = float(intensityVolStr) # check and see if Prec is too big and messes with the parcing. precisionStr = '' if len(precision_line) == 6: #normal line precisionStr = precision_line[5][0:-1] else: precisionStr = precision_line[4][0:-1] precisionPer = float(precisionStr) precision = intensityVol * precisionPer / 100 while not data[n].startswith('SPEC.'): n += 1 specimen_line = data[n].split() specimenDec = specimen_line[2] specimenInc = specimen_line[3] n += 1 geographic_line = data[n] if not geographic_line.startswith('GEOGR'): geographic_dec = '' geographic_inc = '' else: geographic_line = geographic_line.split() geographicDec = geographic_line[1] geographicInc = geographic_line[2] # Add data to various MagIC data tables. specimen = sampleName if specnum != 0: sample = specimen[:specnum] else: sample = specimen site = pmag.parse_site(sample, samp_con, Z) MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {} if specimen != "" and specimen not in [ x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs ]: SpecRec['specimen'] = specimen SpecRec['sample'] = sample SpecRec["citations"] = "This study" SpecRec["analysts"] = user SpecRec['volume'] = volume SpecRecs.append(SpecRec) if sample != "" and sample not in [ x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs ]: SampRec['sample'] = sample SampRec['site'] = site SampRec["citations"] = "This study" SampRec["analysts"] = user SampRec['azimuth'] = specimenAngleDec sample_dip = str(float(specimenAngleInc) - 90.0) #convert to magic orientation SampRec['dip'] = sample_dip SampRec['method_codes'] = meth_code SampRecs.append(SampRec) if site != "" and site not in [ x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs ]: SiteRec['site'] = site SiteRec['location'] = location SiteRec["citations"] = "This study" SiteRec["analysts"] = user SiteRec['lat'] = lat SiteRec['lon'] = lon SiteRecs.append(SiteRec) if location != "" and location not in [ x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs ]: LocRec['location'] = location LocRec["citations"] = "This study" LocRec["analysts"] = user LocRec['lat_n'] = lat LocRec['lon_e'] = lon LocRec['lat_s'] = lat LocRec['lon_w'] = lon LocRecs.append(LocRec) local = pytz.timezone(timezone) naive = datetime.datetime.strptime(date, "%m-%d-%Y:%H:%M:%S") local_dt = local.localize(naive, is_dst=None) utc_dt = local_dt.astimezone(pytz.utc) timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z" MeasRec["specimen"] = specimen MeasRec["timestamp"] = timestamp MeasRec['description'] = '' MeasRec["citations"] = "This study" MeasRec['software_packages'] = version_num MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin MeasRec["quality"] = 'g' MeasRec["standard"] = 'u' MeasRec["treat_step_num"] = '1' MeasRec["treat_ac_field"] = '0' if demagLevel == 'NRM': meas_type = "LT-NO" elif demagLevel[0] == 'A': if demagLevel[:2] == 'AD': treat = float(demagLevel[2:]) else: treat = float(demagLevel[1:]) meas_type = "LT-AF-Z" MeasRec["treat_ac_field"] = '%8.3e' % ( treat * 1e-3) # convert from mT to tesla elif demagLevel[0] == 'T': meas_type = "LT-T-Z" treat = float(demagLevel[1:]) MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin else: print("measurement type unknown", demagLevel) return False, "measurement type unknown" MeasRec["magn_moment"] = str(intensityVol * volume) # Am^2 MeasRec["magn_volume"] = intensityVolStr # A/m MeasRec["dir_dec"] = specimenDec MeasRec["dir_inc"] = specimenInc MeasRec['method_codes'] = meas_type MeasRecs.append(MeasRec) # ignore all the rest of the special characters. Some data files not consistantly formatted. n += 1 while ((len(data[n]) <= 5 and data[n] != '') or data[n].startswith('----')): n += 1 if n >= len(data): break if n >= len(data): # we're done! end = True #end of data while loop con = nb.Contribution(output_dir_path, read_tables=[]) con.add_magic_table_from_data(dtype='specimens', data=SpecRecs) con.add_magic_table_from_data(dtype='samples', data=SampRecs) con.add_magic_table_from_data(dtype='sites', data=SiteRecs) con.add_magic_table_from_data(dtype='locations', data=LocRecs) MeasOuts = pmag.measurements_methods3(MeasRecs, noave) con.add_magic_table_from_data(dtype='measurements', data=MeasOuts) con.tables['specimens'].write_magic_file(custom_name=spec_file) con.tables['samples'].write_magic_file(custom_name=samp_file) con.tables['sites'].write_magic_file(custom_name=site_file) con.tables['locations'].write_magic_file(custom_name=loc_file) con.tables['measurements'].write_magic_file(custom_name=meas_file) return True, meas_file
def convert(**kwargs): # initialize some stuff citations = 'This study' units = 'cgs' meth = "LP-HYS" version_num = pmag.get_version() args = sys.argv Samps, Sites = [], [] noave = 1 # get args user = kwargs.get('user', '') dir_path = kwargs.get('dir_path', '.') output_dir_path = dir_path meas_file = kwargs.get('meas_file', 0) # measurements outfile spec_file = kwargs.get('spec_file', 0) # specimen outfile samp_file = kwargs.get('samp_file', 0) # sample outfile site_file = kwargs.get('site_file', 0) # site outfile loc_file = kwargs.get('loc_file', 0) # location outfile agm_file = kwargs.get('agm_file', '') specnum = kwargs.get('specnum', 0) specimen = kwargs.get('specimen', 0) if not specimen: # grab the specimen name from the input file name specimen = agm_file.split('.')[0] if not meas_file: meas_file = specimen + '.magic' if not spec_file: spec_file = specimen + '_specimens.txt' if not samp_file: samp_file = specimen + '_samples.txt' if not site_file: site_file = specimen + '_sites.txt' if not loc_file: loc_file = specimen + '_locations.txt' samp_con = kwargs.get('samp_con', '1') location = kwargs.get('location', 'unknown') site_infile = kwargs.get('site_infile', '') samp_infile = kwargs.get('samp_infile', '') spec_infile = kwargs.get('spec_infile', '') inst = kwargs.get('ins', '') institution = kwargs.get('institution', '') syn = kwargs.get('syn', 0) syntype = kwargs.get('syntype', '') inst = kwargs.get('ins', '') bak = kwargs.get('bak', 0) units = kwargs.get('units', 0) if bak: meth = "LP-IRM-DCD" output = output_dir_path + "/irm.magic" fmt = kwargs.get('new', 0) xy = kwargs.get('xy', 0) if fmt: fmt = 'new' if not fmt: fmt = 'old' if xy: fmt = 'xy' if specnum != 0: specnum = -specnum if "4" == samp_con[0]: if "-" not in samp_con: print( "naming convention option [4] must be in form 4-Z where Z is an integer") print('---------------') return False, "naming convention option [4] must be in form 4-Z where Z is an integer" else: Z = samp_con.split("-")[1] samp_con = "4" if "7" == samp_con[0]: if "-" not in samp_con: print("option [7] must be in form 7-Z where Z is an integer") return False, "option [7] must be in form 7-Z where Z is an integer" else: Z = samp_con.split("-")[1] samp_con = "7" else: Z = 0 # read stuff in if site_infile: Sites, file_type = pmag.magic_read(site_infile) if samp_infile: Samps, file_type = pmag.magic_read(samp_infile) if spec_infile: Specs, file_type = pmag.magic_read(spec_infile) if agm_file: Data = pmag.open_file(agm_file) if not Data: print("you must provide a valid agm_file") return False, "you must provide a valid agm_file" if not agm_file: print(__doc__) print("agm_file field is required option") return False, "agm_file field is required option" if "ASCII" not in Data[0] and fmt != 'xy': fmt = 'new' measnum, start, end = 1, 0, 0 if fmt == 'new': # new Micromag formatted file end = 2 for skip in range(len(Data)): line = Data[skip] rec = line.strip('\n').strip('\r').split() if 'Units' in line: units = rec[-1] if "Raw" in rec: start = skip + 2 if ("Field" in rec) and ("Moment" in rec) and (not start): start = skip + 2 break elif fmt == 'old': start = 2 end = 1 MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], [] version_num = pmag.get_version() ################################## # parse data stop = len(Data) - end for line in Data[start:stop]: # skip header stuff MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {} # take care of some paper work if syn == 0: MeasRec["specimen"] = specimen if specnum != 0: sample = specimen[:specnum] else: sample = specimen if samp_infile and Samps: # if samp_infile was provided AND yielded sample data samp = pmag.get_dictitem(Samps, 'sample', sample, 'T') if len(samp) > 0: site = samp[0]["site"] else: site = '' if site_infile and Sites: # if samp_infile was provided AND yielded sample data sites = pmag.get_dictitem(Sites, 'sample', sample, 'T') if len(sites) > 0: site = sites[0]["site"] else: site = '' else: site = pmag.parse_site(sample, samp_con, Z) if location != '' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]: LocRec['location'] = location LocRecs.append(LocRec) if site != '' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]: SiteRec['location'] = location SiteRec['site'] = site SiteRecs.append(SiteRec) if sample != '' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]: SampRec['site'] = site SampRec['sample'] = sample SampRecs.append(SampRec) if specimen != '' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]: SpecRec["specimen"] = specimen SpecRec['sample'] = sample SpecRecs.append(SpecRec) else: SampRec["material_type"] = syntype MeasRec["specimen"] = specimen if specnum != 0: sample = specimen[:specnum] else: sample = specimen site = pmag.parse_site(sample, samp_con, Z) if location != '' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]: LocRec['location'] = location LocRecs.append(LocRec) if site != '' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]: SiteRec['location'] = location SiteRec['site'] = site SiteRecs.append(SiteRec) if sample != '' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]: SampRec['site'] = site SampRec['sample'] = sample SampRecs.append(SampRec) if specimen != '' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]: SpecRec["specimen"] = specimen SpecRec['sample'] = sample SpecRecs.append(SpecRec) MeasRec['instrument_codes'] = inst MeasRec['institution'] = institution MeasRec['method_codes'] = meth MeasRec['experiment'] = specimen + ':' + meth if fmt == 'xy': rec = list(line.strip('\n').split()) else: rec = list(line.strip('\n').strip('\r').split(',')) #print (rec) if rec[0] != "": if units == 'cgs': field = float(rec[0]) * 1e-4 # convert from oe to tesla else: field = float(rec[0]) # field in tesla if meth == "LP-HYS": MeasRec['meas_field_dc'] = '%10.3e' % (field) MeasRec['treat_dc_field'] = '0' else: MeasRec['meas_field_dc'] = '0' MeasRec['treat_dc_field'] = '%10.3e' % (field) if units == 'cgs': MeasRec['magn_moment'] = '%10.3e' % ( float(rec[1]) * 1e-3) # convert from emu to Am^2 else: MeasRec['magn_moment'] = '%10.3e' % (float(rec[1])) # Am^2 MeasRec['treat_temp'] = '273' # temp in kelvin MeasRec['meas_temp'] = '273' # temp in kelvin MeasRec['quality'] = 'g' MeasRec['standard'] = 'u' MeasRec['treat_step_num'] = '%i' % (measnum) MeasRec['measurement'] = specimen + ":" + meth + '%i' % (measnum) measnum += 1 MeasRec['software_packages'] = version_num MeasRec['description'] = "" MeasRecs.append(MeasRec) # we have to relabel LP-HYS method codes. initial loop is LP-IMT, minor # loops are LP-M - do this in measurements_methods function if meth == 'LP-HYS': recnum = 0 while float(MeasRecs[recnum]['meas_field_dc']) < float(MeasRecs[recnum + 1]['meas_field_dc']) and recnum + 1 < len(MeasRecs): # this is LP-IMAG MeasRecs[recnum]['method_codes'] = 'LP-IMAG' MeasRecs[recnum]['experiment'] = MeasRecs[recnum]['specimen'] + \ ":" + 'LP-IMAG' recnum += 1 # con = nb.Contribution(output_dir_path, read_tables=[]) # create MagIC tables con.add_magic_table_from_data(dtype='specimens', data=SpecRecs) con.add_magic_table_from_data(dtype='samples', data=SampRecs) con.add_magic_table_from_data(dtype='sites', data=SiteRecs) con.add_magic_table_from_data(dtype='locations', data=LocRecs) # MeasOuts=pmag.measurements_methods3(MeasRecs,noave) con.add_magic_table_from_data(dtype='measurements', data=MeasRecs) # write MagIC tables to file con.write_table_to_file('specimens', custom_name=spec_file) con.write_table_to_file('samples', custom_name=samp_file) con.write_table_to_file('sites', custom_name=site_file) con.write_table_to_file('locations', custom_name=loc_file) con.write_table_to_file('measurements', custom_name=meas_file) return True, meas_file