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
