def main():
"""
NAME
find_azpl.py
DESCRIPTION
finds az,pl that converts CDEC,CINC to GDEC,GINC
SYNTAX
find_azpl.py [command line options] [< filename]
OPTIONS
-f FILE, input file
INPUT
CDEC CINC GDEC GINC
OUTPUT
AZ,PL
"""
out=""
UP=0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
dat=[]
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
input=f.readlines()
else:
input = sys.stdin.readlines() # read from standard input
for line in input:
rec=line.split()
cd,ci,gd,gi=float(rec[0]),float(rec[1]),float(rec[2]),float(rec[3])
az,pl=pmag.get_azpl(cd,ci,gd,gi)
print '%7.1f %7.1f'%(az,pl)
def main():
"""
NAME
generic_magic.py
DESCRIPTION
converts magnetometer files in generic format to magic_measurements format
SYNTAX
generic_magic.py [command line options]
OPTIONS
-h
prints the help message and quits.
-usr USER
identify user, default is ""
-f FILE:
specify path to input file, required
-fsa SAMPFILE:
specify er_samples.txt file for sample orientation data. default is er_samples.txt
-F FILE
specify output file, default is magic_measurements.txt
???-Fsy: specify er_synthetics file, default is er_sythetics.txt
#-Fsa:
# specify output er_samples file, default is NONE
-exp EXPERIMENT-TYPE
Demag:
AF and/or Thermal
PI:
paleointenisty thermal experiment (ZI/IZ/IZZI)
ATRM n:
ATRM in n positions
AARM n:
AARM in n positions
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,.....xx -A
where xx, yyy,zzz...xxx are cooling rates in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70
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 evraged.
But users need to make sure that there are no duplicate meaurements in the file
NLT:
non-linear-TRM experiment
-samp X Y
specimen-sample naming convention.
X=0 Y=n: specimen is distiguished from sample by n initial characters.
(example: if n=4 then and specimen = mgf13a then sample = mgf13)
X=1 Y=n: specimen is distiguished from sample by n terminate characters.
(example: if n=1 then and specimen = mgf13a then sample = mgf13)
X=2 Y=c: specimen is distiguishing from sample by a delimiter.
(example: if c=- then annd specimen = mgf13-a then sample = mgf13)
-site X Y
sample-site naming convention.
X=0 Y=n: sample is distiguished from site by n initial characters.
(example: if n=3 then and sample = mgf13 then sample = mgf)
X=1 Y=n: sample is distiguished from site by n terminate characters.
(example: if n=2 and sample = mgf13 then site = mgf)
X=2 Y=c: specimen is distiguishing from sample by a delimiter.
(example: if c='-' and sample = 'mgf-13' then site = mgf)
-loc LOCNAM
specify location/study name.
-dc B PHI THETA:
B: dc lab field (in micro tesla)
PHI (declination). takes numbers from 0 to 360
THETA (inclination). takes numbers from -90 to 90
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment.
-A: don't average replicate measurements. Take the last measurement from replicate measurements.
-WD working directory
INPUT
A generic file is a tab-delimited file. Each columns should have a header.
The file must include the follwing headers. The order of the columns is not important.
specimen:
string specifying specimen name
treatment:
a number with one or two decimal point (X.Y)
coding for thermal demagnetization:
0.0 or 0 is NRM.
X is temperature in celcsius
Y is always 0
coding for AF demagnetization:
0.0 or 0 is NRM.
X is AF peak field in mT
Y is always 0
coding for Thellier-type experiment:
0.0 or 0 is NRM
X is temperature in celcsius
Y=0: zerofield
Y=1: infield
Y=2: pTRM check
Y=3: pTRM tail check
Y=4: Additivity check
# Ron, Add also 5 for Thellier protocol
treatment_type:
N: NRM
A: AF
T: Thermal
moment:
magnetic moment in emu !!
In addition. at least one of the following headers are requiered:
dec_s:
declination in specimen coordinate system (0 to 360)
inc_s:
inclination in specimen coordinate system (-90 to 90)
Testing:
1) make a genetric file with AF
2) make a genetric file with Thermal
3) make a genetric file with Thermal + AF
4) make a genetric file with IZZI
5) check duplicates option
"""
#--------------------------------------
# functions
#--------------------------------------
def sort_magic_file(path,ignore_lines_n,sort_by_this_name):
'''
reads a file with headers. Each line is stored as a dictionary following the headers.
Lines are sorted in DATA by the sort_by_this_name header
DATA[sort_by_this_name]=[dictionary1,dictionary2,...]
'''
DATA={}
fin=open(path,'rU')
#ignore first lines
for i in range(ignore_lines_n):
fin.readline()
#header
line=fin.readline()
header=line.strip('\n').split('\t')
#print header
for line in fin.readlines():
if line[0]=="#":
continue
tmp_data={}
tmp_line=line.strip('\n').split('\t')
#print tmp_line
for i in range(len(tmp_line)):
if i>= len(header):
continue
tmp_data[header[i]]=tmp_line[i]
DATA[tmp_data[sort_by_this_name]]=tmp_data
fin.close()
return(DATA)
def read_generic_file(path,average_replicates):
'''
reads a generic file format. If average_replicates==True average replicate measurements.
Rrturns a Data dictionary with measurements line sorted by specimen
Data[specimen_name][dict1,dict2,...]
'''
Data={}
Fin=open(path,'rU')
header=Fin.readline().strip('\n').split('\t')
duplicates=[]
for line in Fin.readlines():
tmp_data={}
#found_duplicate=False
l=line.strip('\n').split('\t')
for i in range(min(len(header),len(l))):
tmp_data[header[i]]=l[i]
specimen=tmp_data['specimen']
if specimen not in Data.keys():
Data[specimen]=[]
Data[specimen].append(tmp_data)
# search fro duplicates
for specimen in Data.keys():
x=len(Data[specimen])-1
new_data=[]
duplicates=[]
for i in range(1,x):
while i< len(Data[specimen]) and Data[specimen][i]['treatment']==Data[specimen][i-1]['treatment'] and Data[specimen][i]['treatment_type']==Data[specimen][i-1]['treatment_type']:
duplicates.append(Data[specimen][i])
del(Data[specimen][i])
if len(duplicates)>0:
if average_replicates:
duplicates.append(Data[specimen][i-1])
Data[specimen][i-1]=average_duplicates(duplicates)
print "-W- WARNING: averaging %i duplicates for specimen %s treatmant %s"%(len(duplicates),specimen,duplicates[-1]['treatment'])
duplicates=[]
else:
Data[specimen][i-1]=duplicates[-1]
print "-W- WARNING: found %i duplicates for specimen %s treatmant %s. Taking the last measurement only"%(len(duplicates),specimen,duplicates[-1]['treatment'])
duplicates=[]
if i==len(Data[specimen])-1:
break
# if tmp_data['treatment']==Data[specimen][-1]['treatment'] and tmp_data['treatment_type']==Data[specimen][-1]['treatment_type']:
#
## check replicates
#if tmp_data['treatment']==Data[specimen][-1]['treatment'] and tmp_data['treatment_type']==Data[specimen][-1]['treatment_type']:
# #found_duplicate=True
# duplicates.append(Data[specimen][-1])
# duplicates.append(tmp_data)
# del(Data[specimen][-1])
# continue
#else:
# if len(duplicates)>0:
# if average_replicates:
# Data[specimen].append(average_duplicates(duplicates))
# print "-W- WARNING: averaging %i duplicates for specimen %s treatmant %s"%(len(duplicates),specimen,duplicates[-1]['treatment'])
# else:
# Data[specimen].append(duplicates[-1])
# print "-W- WARNING: found %i duplicates for specimen %s treatmant %s. Taking the last measurement only"%(len(duplicates),specimen,duplicates[-1]['treatment'])
# duplicates=[]
# Data[specimen].append(tmp_data)
return(Data)
def average_duplicates(duplicates):
'''
avarage replicate measurements.
'''
carts_s,carts_g,carts_t=[],[],[]
for rec in duplicates:
moment=float(rec['moment'])
if 'dec_s' in rec.keys() and 'inc_s' in rec.keys():
if rec['dec_s']!="" and rec['inc_s']!="":
dec_s=float(rec['dec_s'])
inc_s=float(rec['inc_s'])
cart_s=pmag.dir2cart([dec_s,inc_s,moment])
carts_s.append(cart_s)
if 'dec_g' in rec.keys() and 'inc_g' in rec.keys():
if rec['dec_g']!="" and rec['inc_g']!="":
dec_g=float(rec['dec_g'])
inc_g=float(rec['inc_g'])
cart_g=pmag.dir2cart([dec_g,inc_g,moment])
carts_g.append(cart_g)
if 'dec_t' in rec.keys() and 'inc_t' in rec.keys():
if rec['dec_t']!="" and rec['inc_t']!="":
dec_t=float(rec['dec_t'])
inc_t=float(rec['inc_t'])
cart_t=pmag.dir2cart([dec_t,inc_t,moment])
carts_t.append(cart_t)
if len(carts_s)>0:
carts=scipy.array(carts_s)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_s="%.2f"%mean_dir[0]
mean_inc_s="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_s,mean_inc_s="",""
if len(carts_g)>0:
carts=scipy.array(carts_g)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_g="%.2f"%mean_dir[0]
mean_inc_g="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_g,mean_inc_g="",""
if len(carts_t)>0:
carts=scipy.array(carts_t)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_t="%.2f"%mean_dir[0]
mean_inc_t="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_t,mean_inc_t="",""
meanrec={}
for key in duplicates[0].keys():
if key in ['dec_s','inc_s','dec_g','inc_g','dec_t','inc_t','moment']:
continue
else:
meanrec[key]=duplicates[0][key]
meanrec['dec_s']=mean_dec_s
meanrec['dec_g']=mean_dec_g
meanrec['dec_t']=mean_dec_t
meanrec['inc_s']=mean_inc_s
meanrec['inc_g']=mean_inc_g
meanrec['inc_t']=mean_inc_t
meanrec['moment']=mean_moment
return meanrec
def get_upper_level_name(name,nc):
'''
get sample/site name from specimen/sample using naming convention
'''
if float(nc[0])==0:
if float(nc[1])!=0:
number_of_char=int(nc[1])
high_name=name[:number_of_char]
else:
high_name=name
elif float(nc[0])==1:
if float(nc[1])!=0:
number_of_char=int(nc[1])*-1
high_name=name[:number_of_char]
else:
high_name=name
elif float(nc[0])==2:
d=str(nc[1])
name_splitted=name.split(d)
if len(name_splitted)==1:
high_name=name_splitted[0]
else:
high_name=d.join(name_splitted[:-1])
else:
high_name=name
return high_name
def merge_pmag_recs(old_recs):
recs={}
recs=copy.deepcopy(old_recs)
headers=[]
for rec in recs:
for key in rec.keys():
if key not in headers:
headers.append(key)
for rec in recs:
for header in headers:
if header not in rec.keys():
rec[header]=""
return recs
#--------------------------------------
# get command line arguments
#--------------------------------------
args=sys.argv
user=""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
else:
user=""
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
else:
samp_file="er_samples.txt"
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file:",magfile
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
labfield_phi=float(args[ind+2])
labfield_theta=float(args[ind+3])
if '-exp' in args:
ind=args.index("-exp")
experiment=args[ind+1]
else:
print "-LP is required option"
print main.__doc__
sys.exit()
if experiment=='ATRM':
ind=args.index("ATRM")
atrm_n_pos=int(args[ind+1])
if experiment=='AARM':
ind=args.index("AARM")
aarm_n_pos=int(args[ind+1])
if experiment=='CR':
ind=args.index("CR")
coolling_times=args[ind+1]
coolling_times_list=coolling_times.split(',')
if "-samp" in args:
ind=args.index("-samp")
sample_nc=[]
sample_nc.append(args[ind+1])
sample_nc.append(args[ind+2])
if "-site" in args:
ind=args.index("-site")
site_nc=[]
site_nc.append(args[ind+1])
site_nc.append(args[ind+2])
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
else:
er_location_name=""
if "-A" in args:
noave=1
else:
noave=0
if "-WD" in args:
ind=args.index("-WD")
WD=args[ind+1]
os.chdir(WD)
#--------------------------------------
# read data from er_samples.txt
#--------------------------------------
#if "-fsa" in args:
# ind=args.index("-fsa")
# er_sample_file=args[ind+1]
#else:
# er_sample_file="er_samples.txt"
er_sample_data={}
#er_sample_data=sort_magic_file(samp_file,1,'er_sample_name')
try:
er_sample_data=sort_magic_file(samp_file,1,'er_sample_name')
print "-I- Found er_samples.txt"
print '-I- sample information will be appended to existing er_samples.txt file'
except:
print "-I- Cant find file er_samples.txt"
print '-I- sample information will be stored in new er_samples.txt file'
#--------------------------------------
# read data from generic file
#--------------------------------------
if noave:
mag_data=read_generic_file(magfile,False)
else:
mag_data=read_generic_file(magfile,True)
#--------------------------------------
# for each specimen get the data, and translate it to MagIC format
#--------------------------------------
ErSamplesRecs=[]
MagRecs=[]
specimens_list=mag_data.keys()
specimens_list.sort()
for specimen in specimens_list:
measurement_running_number=0
this_specimen_treatments=[] # a list of all treatments
MagRecs_this_specimen=[]
LP_this_specimen=[] # a list of all lab protocols
IZ,ZI=0,0 # counter for IZ and ZI steps
for meas_line in mag_data[specimen]:
#------------------
# trivial MagRec data
#------------------
MagRec={}
MagRec['er_citation_names']="This study"
MagRec["er_specimen_name"]=meas_line['specimen']
MagRec["er_sample_name"]=get_upper_level_name(MagRec["er_specimen_name"],sample_nc)
MagRec["er_site_name"]=get_upper_level_name(MagRec["er_sample_name"],site_nc)
MagRec['er_location_name']=er_location_name
MagRec['er_analyst_mail_names']=user
MagRec["magic_instrument_codes"]=""
MagRec["measurement_flag"]='g'
MagRec["measurement_number"]="%i"%measurement_running_number
MagRec["measurement_magn_moment"]='%10.3e'%(float(meas_line["moment"])*1e-3) # in Am^2
MagRec["measurement_temp"]='273.' # room temp in kelvin
#------------------
# decode treatments from treatment column in the generic file
#------------------
treatment=[]
treatment_code=str(meas_line['treatment']).split(".")
treatment.append(float(treatment_code[0]))
if len(treatment_code)==1:
treatment.append(0)
else:
treatment.append(float(treatment_code[1]))
#------------------
# lab field direction
#------------------
if experiment in ['PI','NLT','CR']:
if float(treatment[1])==0:
MagRec["treatment_dc_field"]="0"
MagRec["treatment_dc_field_phi"]="0"
MagRec["treatment_dc_field_theta"]="0"
else:
MagRec["treatment_dc_field"]='%8.3e'%(float(labfield))
MagRec["treatment_dc_field_phi"]="%.2f"%(float(labfield_phi))
MagRec["treatment_dc_field_theta"]="%.2f"%(float(labfield_theta))
else:
MagRec["treatment_dc_field"]=""
MagRec["treatment_dc_field_phi"]=""
MagRec["treatment_dc_field_theta"]=""
#------------------
# treatment temperature/peak field
#------------------
if experiment == 'Demag':
if meas_line['treatment_type']=='A':
MagRec['treatment_temp']="273."
MagRec["treatment_ac_field"]="%.3e"%(treatment[0]*1e-3)
elif meas_line['treatment_type']=='N':
MagRec['treatment_temp']="273."
MagRec["treatment_ac_field"]=""
else:
MagRec['treatment_temp']="%.2f"%(treatment[0]+273.)
MagRec["treatment_ac_field"]=""
else:
MagRec['treatment_temp']="%.2f"%(treatment[0]+273.)
MagRec["treatment_ac_field"]=""
#---------------------
# Lab treatment
# Lab protocol
#---------------------
#---------------------
# Lab treatment and lab protocoal for NRM:
#---------------------
if float(meas_line['treatment'])==0:
LT="LT-NO"
LP="" # will be filled later after finishing reading all measurements line
#---------------------
# Lab treatment and lab protocoal for paleointensity experiment
#---------------------
elif experiment =='PI':
LP="LP-PI-TRM"
if treatment[1]==0:
LT="LT-T-Z"
elif treatment[1]==1 or treatment[1]==10: # infield
LT="LT-T-I"
elif treatment[1]==2 or treatment[1]==20: # pTRM check
LT="LT-PTRM-I"
LP=LP+":"+"LP-PI-ALT-PTRM"
elif treatment[1]==3 or treatment[1]==30: # Tail check
LT="LT-PTRM-MD"
LP=LP+":"+"LP-PI-BT-MD"
elif treatment[1]==4 or treatment[1]==40: # Additivity check
LT="LT-PTRM-AC"
LP=LP+":"+"LP-PI-BT-MD"
else:
print "-E- unknown measurement code specimen %s treatmemt %s"%(meas_line['specimen'],meas_line['treatment'])
MagRec={}
continue
# save all treatment in a list
# we will use this later to distinguidh between ZI / IZ / and IZZI
this_specimen_treatments.append(float(meas_line['treatment']))
if LT=="LT-T-Z":
if float(treatment[0]+0.1) in this_specimen_treatments:
LP=LP+":"+"LP-PI-IZ"
if LT=="LT-T-I":
if float(treatment[0]+0.0) in this_specimen_treatments:
LP=LP+":"+"LP-PI-ZI"
#---------------------
# Lab treatment and lab protocoal for demag experiment
#---------------------
elif "Demag" in experiment:
if meas_line['treatment_type']=='A':
LT="LT-AF-Z"
LP="LP-DIR-AF"
else:
LT="LT-T-Z"
LP="LP-DIR-T"
#---------------------
# Lab treatment and lab protocoal for ATRM experiment
#---------------------
elif experiment in ['ATRM','AARM']:
if experiment=='ATRM':
LP="LP-AN-TRM"
n_pos=atrm_n_pos
if n_pos!=6:
print "the program does not support ATRM in %i position."%n_pos
continue
if experiment=='AARM':
#MagRec['treatment_temp']="273."
#MagRec["treatment_ac_field"]=""
LP="LP-AN-ARM"
n_pos=aarm_n_pos
if n_pos!=6:
print "the program does not support AARM in %i position."%n_pos
continue
if treatment[1]==0:
if experiment=='ATRM':
LT="LT-T-Z"
MagRec['treatment_temp']="%.2f"%(treatment[0]+273.)
MagRec["treatment_ac_field"]=""
else:
LT="LT-AF-Z"
MagRec['treatment_temp']="273."
MagRec["treatment_ac_field"]="%.3e"%(treatment[0]*1e-3)
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
if experiment=='ATRM':
if float(treatment[1])==70 or float(treatment[1])==7: # alteration check as final measurement
LT="LT-PTRM-I"
else:
LT="LT-T-I"
else:
LT="LT-AF-I"
MagRec["treatment_dc_field"]='%8.3e'%(float(labfield))
# 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)
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
if treatment[1] < 10:
ipos_code=int(treatment[1])-1
else:
ipos_code=int(treatment[1]/10)-1
# (2) using the magnetization
if meas_line["dec_s"]!="":
DEC=float(meas_line["dec_s"])
INC=float(meas_line["inc_s"])
elif meas_line["dec_g"]!="":
DEC=float(meas_line["dec_g"])
INC=float(meas_line["inc_g"])
elif meas_line["dec_t"]!="":
DEC=float(meas_line["dec_t"])
INC=float(meas_line["inc_t"])
if DEC<0 and DEC>-359:
DEC=360.+DEC
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
# check it
if treatment[1]!= 7 and treatment[1]!= 70:
if ipos_guess!=ipos_code:
print "-W- WARNING: check specimen %s step %s, anistropy measurements, coding does not match the direction of the lab field"%(specimen,meas_line['treatment'])
MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc[ipos])
#---------------------
# Lab treatment and lab protocoal for cooling rate experiment
#---------------------
elif experiment == "CR":
coolling_times_list
LP="LP-CR-TRM"
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
if treatment[1]==0:
LT="LT-T-Z"
MagRec["treatment_dc_field"]="0"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
if treatment[1]==7: # alteration check as final measurement
LT="LT-PTRM-I"
else:
LT="LT-T-I"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f' % (labfield_phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (labfield_theta) # labfield theta
indx=int(treatment[1])-1
# alteration check matjed as 0.7 in the measurement file
if indx==6:
cooling_time= coolling_times_list[-1]
else:
cooling_time=coolling_times_list[indx]
MagRec["measurement_description"]="cooling_rate"+":"+cooling_time+":"+"K/min"
#---------------------
# Lab treatment and lab protocoal for NLT experiment
#---------------------
elif 'NLT' in experiment :
print "Dont support yet NLT rate experiment file. Contact [email protected]"
#---------------------
# magic_method_codes for this measurement only
# LP will be fixed after all measurement lines are read
#---------------------
MagRec["magic_method_codes"]=LT+":"+LP
#---------------------
# Demag experiments only:
# search if orientation data exists in er_samples.txt
# if not: create one and save
#---------------------
# see if core azimuth and tilt-corrected data are in er_samples.txt
sample=MagRec["er_sample_name"]
found_sample_azimuth,found_sample_dip,found_sample_bed_dip_direction,found_sample_bed_dip=False,False,False,False
if sample in er_sample_data.keys():
if "sample_azimuth" in er_sample_data[sample].keys() and er_sample_data[sample]['sample_azimuth'] !="":
sample_azimuth=float(er_sample_data[sample]['sample_azimuth'])
found_sample_azimuth=True
if "sample_dip" in er_sample_data[sample].keys() and er_sample_data[sample]['sample_dip']!="":
sample_dip=float(er_sample_data[sample]['sample_dip'])
found_sample_dip=True
if "sample_bed_dip_direction" in er_sample_data[sample].keys() and er_sample_data[sample]['sample_bed_dip_direction']!="":
sample_bed_dip_direction=float(er_sample_data[sample]['sample_bed_dip_direction'])
found_sample_bed_dip_direction=True
if "sample_bed_dip" in er_sample_data[sample].keys() and er_sample_data[sample]['sample_bed_dip']!="":
sample_bed_dip=float(er_sample_data[sample]['sample_bed_dip'])
found_sample_bed_dip=True
else:
er_sample_data[sample]={}
#--------------------
# deal with specimen orientation and different coordinate system
#--------------------
found_s,found_geo,found_tilt=False,False,False
if "dec_s" in meas_line.keys() and "inc_s" in meas_line.keys():
if meas_line["dec_s"]!="" and meas_line["inc_s"]!="":
found_s=True
MagRec["measurement_dec"]=meas_line["dec_s"]
MagRec["measurement_inc"]=meas_line["inc_s"]
if "dec_g" in meas_line.keys() and "inc_g" in meas_line.keys():
if meas_line["dec_g"]!="" and meas_line["inc_g"]!="":
found_geo=True
if "dec_t" in meas_line.keys() and "inc_t" in meas_line.keys():
if meas_line["dec_t"]!="" and meas_line["inc_t"]!="":
found_tilt=True
#-----------------------------
# specimen coordinates: no
# geographic coordinates: yes
#-----------------------------
if found_geo and not found_s:
MagRec["measurement_dec"]=meas_line["dec_g"]
MagRec["measurement_inc"]=meas_line["inc_g"]
# core azimuth/plunge is not in er_samples.txt
if not found_sample_dip or not found_sample_azimuth:
er_sample_data[sample]['sample_azimuth']="0"
er_sample_data[sample]['sample_dip']="0"
# core azimuth/plunge is in er_samples.txt
else:
sample_azimuth=float(er_sample_data[sample]['sample_azimuth'])
sample_dip=float(er_sample_data[sample]['sample_dip'])
if sample_azimuth!=0 and sample_dip!=0:
print "-W- WARNING: delete core azimuth/plunge in er_samples.txt\n\
becasue dec_s and inc_s are unavaialable"
#-----------------------------
# specimen coordinates: no
# geographic coordinates: no
#-----------------------------
if not found_geo and not found_s:
print "-E- ERROR: sample %s does not have dec_s/inc_s or dec_g/inc_g. Ignore specimen %s "%(sample,specimen)
break
#-----------------------------
# specimen coordinates: yes
# geographic coordinates: yes
#
# commant: Ron, this need to be tested !!
#-----------------------------
if found_geo and found_s:
cdec,cinc=float(meas_line["dec_s"]),float(meas_line["inc_s"])
gdec,ginc=float(meas_line["dec_g"]),float(meas_line["inc_g"])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
# core azimuth/plunge is not in er_samples.txt:
# calculate core az/pl and add it to er_samples.txt
if not found_sample_dip or not found_sample_azimuth:
er_sample_data[sample]['sample_azimuth']="%.1f"%az
er_sample_data[sample]['sample_dip']="%.1f"%pl
# core azimuth/plunge is in er_samples.txt
else:
if float(er_sample_data[sample]['sample_azimuth'])!= az:
print "-E- ERROR in sample_azimuth sample %s. Check it! using the value in er_samples.txt"%sample
if float(er_sample_data[sample]['sample_dip'])!= pl:
print "-E- ERROR in sample_dip sample %s. Check it! using the value in er_samples.txt"%sample
#-----------------------------
# specimen coordinates: yes
# geographic coordinates: no
#-----------------------------
if not found_geo and found_s:
if found_sample_dip and found_sample_azimuth:
pass
# (nothing to do)
else:
if "Demag" in experiment:
print "-W- WARNING: missing sample_dip or sample_azimuth for sample %s"%sample
#-----------------------------
# tilt-corrected coordinates: yes
# geographic coordinates: no
#-----------------------------
if found_tilt and not found_geo:
print "-E- ERROR: missing geographic data for sample %s. Ignoring tilt-corrected data "%sample
if found_tilt and found_geo:
dec_geo,inc_geo=float(meas_line["dec_g"]),float(meas_line["inc_g"])
dec_tilt,inc_tilt=float(meas_line["dec_t"]),float(meas_line["inc_t"])
if dec_geo==dec_tilt and inc_geo==inc_tilt:
DipDir,Dip=0.,0.
else:
DipDir,Dip=pmag.get_tilt(dec_geo,inc_geo,dec_tilt,inc_tilt)
if not found_sample_bed_dip_direction or not found_sample_bed_dip:
print "-I- calculating dip and dip direction used for tilt correction sample %s. results are put in er_samples.txt"%sample
er_sample_data[sample]['sample_bed_dip_direction']="%.1f"%DipDir
er_sample_data[sample]['sample_bed_dip']="%.1f"%Dip
#-----------------------------
# er_samples method codes
# geographic coordinates: no
#-----------------------------
if found_tilt or found_geo:
er_sample_data[sample]['magic_method_codes']="SO-NO"
#-----------------
# er_samples_data
#-----------------
if sample in er_sample_data.keys():
er_sample_data[sample]['er_sample_name']=sample
er_sample_data[sample]['er_site_name']=MagRec["er_site_name"]
er_sample_data[sample]['er_location_name']=MagRec["er_location_name"]
#MagRec["magic_method_codes"]=LT
MagRecs_this_specimen.append(MagRec)
#if LP!="" and LP not in LP_this_specimen:
# LP_this_specimen.append(LP)
measurement_running_number+=1
#-------
#-------
# after reading all the measurements lines for this specimen
# 1) add magic_experiment_name
# 2) fix magic_method_codes with the correct lab protocol
#-------
LP_this_specimen=[]
for MagRec in MagRecs_this_specimen:
magic_method_codes=MagRec["magic_method_codes"].split(":")
for code in magic_method_codes:
if "LP" in code and code not in LP_this_specimen:
LP_this_specimen.append(code)
# check IZ/ZI/IZZI
if "LP-PI-ZI" in LP_this_specimen and "LP-PI-IZ" in LP_this_specimen:
LP_this_specimen.remove("LP-PI-ZI")
LP_this_specimen.remove("LP-PI-IZ")
LP_this_specimen.append("LP-PI-BT-IZZI")
# add the right LP codes and fix experiment name
for MagRec in MagRecs_this_specimen:
MagRec["magic_experiment_name"]=MagRec["er_specimen_name"]+":"+":".join(LP_this_specimen)
magic_method_codes=MagRec["magic_method_codes"].split(":")
LT=""
for code in magic_method_codes:
if code[:3]=="LT-":
LT=code;
break
MagRec["magic_method_codes"]=LT+":"+":".join(LP_this_specimen)
MagRecs.append(MagRec)
#--
# write magic_measurements.txt
#--
MagRecs_fixed=merge_pmag_recs(MagRecs)
pmag.magic_write(meas_file,MagRecs_fixed,'magic_measurements')
print "-I- MagIC file is saved in %s"%meas_file
#--
# write er_samples.txt
#--
ErSamplesRecs=[]
samples=er_sample_data.keys()
samples.sort()
for sample in samples:
ErSamplesRecs.append(er_sample_data[sample])
ErSamplesRecs_fixed=merge_pmag_recs(ErSamplesRecs)
pmag.magic_write("er_samples.txt",ErSamplesRecs_fixed,'er_samples')
def main():
"""
NAME
UCSC_leg_magic.py
DESCRIPTION
converts UCSC legacy format files to magic_measurements format files
SYNTAX
UCSC_leg_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, or
-fin INDEX: specify index file for reading whole directory: default is index.txt
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-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] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
INPUT
Format of UCSC legacy files:
Spec Treat CDec CInc GDec GInc SDec SInc Int [optional A95]
Treat is HX where X is AF field in Oe, TX where X is T in C, or NRM
Intensity assumed to be total moment in (emu/cc) with a 10cc specimen volume
CDec: Declination in specimen coordinate system
CInc: Declination in specimen coordinate system
GDec: Declination in geographic coordinate system
GInc: Declination in geographic coordinate system
SDec: Declination in stratigraphic coordinate system
SInc: Declination in stratigraphic coordinate system
index file: must be formatted:
FILENAME SITE
"""
# initialize some stuff
noave=0
methcode,inst="",""
samp_con,Z='4',3
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
#
# get command line arguments
#
user=""
mag_file=""
ind_file=""
dir_path='.'
ErSamps,ErSites=[],[]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
samp_file=dir_path+'/er_samples.txt'
site_file=dir_path+'/er_sites.txt'
meas_file=dir_path+"/magic_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-Fsi' in args:
ind=args.index("-Fsi")
site_file=dirpath+'.'+args[ind+1]
try:
open(site_file,'rU')
ErSites,file_type=pmag.magic_read(site_file)
print 'site information will be appended to ', site_file
except:
print site_file,' not found: site information will be stored in new er_sites.txt file'
site_file=dir_path+'/er_sites.txt'
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dirpath+'/'+args[ind+1]
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
print 'sample information will be appended to ', samp_file
except:
print samp_file,' not found: sample information will be stored in new er_samples.txt file'
samp_file=dir_path+'/er_samples.txt'
if '-f' in args:
ind=args.index("-f")
mag_file=args[ind+1]
site=mag_file.split('.')[0]
magfile=dir_path+'/'+mag_file
try:
input=open(magfile,'rU')
MagFiles.append([magfile,site])
except:
print "bad input file name"
sys.exit()
elif '-fin' in args:
ind=args.index("-fin")
ind_file=args[ind+1]
ind_file=dir_path+'/'+ind_file
try:
index_file=open(ind_file,'rU')
except:
print "bad index file name"
sys.exit()
elif '-fin' not in args:
ind_file=dir_path+'/index.txt'
try:
index_file=open(ind_file,'rU')
except:
print "bad index file name"
sys.exit()
if ind_file!="":
Files=index_file.readlines()
for file in Files:
rec=file.split()
MagFiles.append(rec)
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
else:
print "-loc is required option"
print main.__doc__
sys.exit()
if "-A" in args: noave=1
Sites=[]
for file in MagFiles:
site=file[1] # attach site name either from file name or from index file
if site not in Sites:
Sites.append(site)
ErSiteRec={'er_location_name': er_location_name,'er_site_name':site,'er_citation_names':citation,'site_definition':'s','site_lat':'','site_lon':"",'site_class':"",'site_lithology':"",'site_type':""}
ErSites.append(ErSiteRec)
print 'processing file: ',file[0],' for site: ',site
data=open(dir_path+'/'+file[0],'rU').readlines() # read in data from file
firstrec=data[0].split()
if firstrec[0]=='FILE': # this file has a header, must look for start of data
for k in range(len(data)):
if data[k][0]=='-': break
else:
k=-1
while k<len(data)-1:
k+=1
line=data[k]
if len(line)>2: # skip stupid terminal lines
line=line.replace(' T ',' T') # make columns consistent
line=line.replace(' H ',' H') # make columns consistent
line=line.replace(' T ',' T') # make columns consistent
line=line.replace(' H ',' H') # make columns consistent
rec=line.split()
if len(rec)<2: break # skip junk
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'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
# site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[8])*1e-4) # # int is in emu/cc; assuming 10cc, this converts to Am^2
#
if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
cdec,cinc=float(rec[2]),float(rec[3])
gdec,ginc=float(rec[4]),float(rec[5])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
bdec,binc=float(rec[6]),float(rec[7])
if rec[4]!=rec[6] and rec[5]!=rec[7]:
dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
else:
dipdir,dip=0,0
ErSampRec={}
ErSampRec['er_citation_names']='This study'
ErSampRec['er_location_name']=MagRec['er_location_name']
ErSampRec['er_site_name']=MagRec['er_site_name']
ErSampRec['er_sample_name']=MagRec['er_sample_name']
ErSampRec['sample_azimuth']='%7.1f'%(az)
ErSampRec['sample_dip']='%7.1f'%(pl)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in UCSC legacy file'
ErSampRec['magic_method_codes']='SO-NO'
ErSamps.append(ErSampRec)
Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"]=rec[2]
MagRec["measurement_inc"]=rec[3]
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
demag=rec[1][0]
if demag!='N':
treat=float(rec[1][1:])
else:
treat=0
if demag=="H":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-4) # convert from oe to tesla
meas_type="LT-AF-Z"
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "sample orientations put in ",samp_file
pmag.magic_write(site_file,ErSites,'er_sites')
print "site names put in ",site_file
def main():
"""
NAME
UCSC_magic.py
DESCRIPTION
converts UCSC format files to MagIC formatted files
SYNTAX
UCSC_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify UCSC format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-A: don't average replicate measurements
"""
global k,Data
k,Data,measNum=0,[],0
ErLocs,ErSites,ErSamps,ErSpecs,MagRecs=[],[],[],[],[] # MagIC formatted info
# initialize some stuff
noave=0
args=sys.argv
ErLocs,ErSites,ErSamps,ErSpecs,MagicMeas=[],[],[],[],[] # MagIC formatted info
dir_path='.'
#
# get command line arguments
#
if '-WD' in args: # set working directory (only for within MagIC.py GUI)
ind=args.index("-WD")
dir_path=args[ind+1]
loc_file,site_file,samp_file,spec_file,meas_file=dir_path+"/er_locations.txt",dir_path+"/er_sites.txt",dir_path+"/er_samples.txt",dir_path+"/er_specimens.txt",dir_path+"/magic_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=dir_path+'/'+args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-A" in args: noave=1
InData=input.readlines()
Data=[]
for line in InData:
if line!="\n" and line!="":
Data.append(line) # strip out annoying blank lines
LocRec=parseloc() # peel off the location info
ErLoc={}
ErLoc['er_location_name']=LocRec['name']
ErLoc['er_citation_name']="This study"
ErLoc['location_type']="outcrop"
ErLoc['location_begin_lat']=LocRec['northLatitude']
ErLoc['location_begin_lon']=LocRec['eastLongitude']
ErLoc['location_begin_elevation']=convert2meters(LocRec['altitude'],LocRec['altitudeUnits'])
ErLoc['location_description']=LocRec['comments']
ErLocs.append(ErLoc)
while "</locality>" not in Data[k]:
ErSite={}
SiteRec=parsesite()
if SiteRec=='done': break
print SiteRec['name']
ErSite['er_citation_name']="This study"
ErSite['er_location_name']=ErLoc['er_location_name']
ErSite['site_definition']='s' # this means a single site as opposed to composite site
ErSite['er_site_name']=SiteRec['name']
ErSite['site_type']=""
ErSite['site_class']=""
ErSite['site_lithology']=""
ErSite['site_lat']=SiteRec['northLatitude']
ErSite['site_lon']=SiteRec['eastLongitude']
ErSite['site_elevation']=convert2meters(SiteRec['altitude'],SiteRec['altitudeUnits'])
ErSite['site_description']=SiteRec['comments']
ErSites.append(ErSite)
samples=[] # this is a list for unique sample names
while '</site>' not in Data[k] and k<len(Data):
ErSpec={}
SpecRec=parsespec()
print SpecRec['name']
ErSpec['er_specimen_name']=SpecRec['name']
ErSpec['er_citation_name']="This study"
ErSpec['er_location_name']=ErLoc['er_location_name']
ErSpec['er_citation_names']="This study"
ErSpec['er_site_name']=ErSite['er_site_name']
er_sample_name=ErSpec['er_specimen_name'][:-1]
ErSpec['er_sample_name']=er_sample_name
ErSpec['specimen_volume']=SpecRec['volume'] # volume in m^3
ErSpecs.append(ErSpec)
MeasRecs=parsesteps()
print len(MeasRecs),' measurements'
if er_sample_name not in samples: # new sample name
samples.append(er_sample_name)
ErSamp={}
ErSamp['er_sample_name']=er_sample_name
ErSamp['er_citation_name']="This study"
ErSamp['er_location_name']=ErLoc['er_location_name']
ErSamp['er_site_name']=ErSite['er_site_name']
ErSamp['sample_lat']=ErSite['site_lat']
ErSamp['sample_lon']=ErSite['site_lon']
ErSamp['sample_elevation']=ErSite['site_elevation']
ErSamp['sample_date']=parsedate(SpecRec['dateCollected'])
# ErSamp['sample_time_zone']=LocRec['gmtOffset']+"+GMT"
ErSamp['sample_bed_dip_direction']=str(float(SpecRec['strike'])+90.)
ErSamp['sample_bed_dip']=SpecRec['dip']
ErSamp['sample_height']=SpecRec['stratigraphicLevel']
ErSamp['sample_description']=SpecRec['comments']
ErSamp['sample_declination_correction']=LocRec['regionalDeclination']
if 'calculatedSunAz' in SpecRec.keys():
ErSamp['sample_azimuth']=SpecRec['calculatedSunAz']
ErSamp['magic_method_codes']='SO-SUN'
az,pl=pmag.get_azpl(float(MeasRecs[0]['coreDec']),float(MeasRecs[0]['coreInc']),float(MeasRecs[0]['geoDec']),float(MeasRecs[0]['geoInc']))
ErSamp['sample_azimuth']=str(az)
ErSamp['sample_dip']=str(pl)
ErSamps.append(ErSamp)
for MeasRec in MeasRecs:
MagRec={}
measNum+=1
MagRec['er_citation_names']="This study"
MagRec['measurement_number']='%i'%(measNum)
MagRec['er_location_name']=ErSpec['er_location_name']
MagRec['er_site_name']=ErSpec['er_site_name']
MagRec['er_sample_name']=ErSpec['er_sample_name']
MagRec['er_specimen_name']=ErSpec['er_specimen_name']
MagRec['measurement_date']=parsedate(MeasRec['date'])
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'
step=MeasRec['stepType']
if step=='AF':
MagRec["magic_method_codes"]="LT-AF-Z" # lab treatment, af in zero field
MagRec['magic_experiment_name']=MagRec['er_specimen_name']+":LT-AF-Z"
elif step=="TH": # I'm guessing here
MagRec["magic_method_codes"]="LT-T-Z" # this is "lab treatment, thermal in zero field
MagRec['magic_experiment_name']=MagRec['er_specimen_name']+":LT-T-Z"
else:
MagRec["magic_method_codes"]="LT-NO" # no lab treatment - NRM
MagRec['magic_experiment_name']=MagRec['er_specimen_name']+":LT-NO"
MagRec['measurement_dec']=MeasRec['coreDec']
MagRec['measurement_inc']=MeasRec['coreInc']
MagRec['measurement_magn_volume']=MeasRec['J'] # intensity in A/m
MagRec['measurement_magn_moment']=str(float(MeasRec['J'])*float(ErSpec['specimen_volume'])) # intensity in Am^2
MagRec['measurement_chi_volume']=MeasRec['susceptibility'] # assuming dimensionless SI CHECK THIS
MagRec['magic_software_packages']=MeasRec['measuringRoutine'] #
if step=="AF": MagRec["treatment_ac_field"]=str(1e-3*float(MeasRec['stepLevel'])) # stepLevel in tesla
if step=="TH":
stepLevel=float(MeasRec['stepLevel']) +273
MagRec["treatment_temp"]='%8.3e' % (stepLevel) # treatment step in kelvin
MagRec["measurement_csd"]=MeasRec['Q_95'] # I think this is the csd
MagRec["magic_instrument_codes"]='UCSC-'+MeasRec['instrument']
MagRec["er_analyst_mail_names"]=MeasRec['operator']
MagRec["measurement_flag"]='g' # good measurement flag
MagRec["measurement_standard"]='u' # # unknown - as opposed to standard
MagRecs.append(MagRec)
pmag.magic_write(loc_file,ErLocs,'er_locations')
print "results put in ",loc_file
pmag.magic_write(site_file,ErSites,'er_sites')
print "results put in ",site_file
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "results put in ",samp_file
pmag.magic_write(spec_file,ErSpecs,'er_specimens')
print "results put in ",spec_file
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "results put in ",meas_file
def main():
"""
NAME
LIVMW_magic.py
DESCRIPTION
converts Liverpool microwave format files to magic_measurements format files
SYNTAX
LIVMW_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify liverpool format input file, required
-usr USER: identify user, default is ""
-ins INST: identify instrument, e.g., LIV-TRISTAN, LIV-OLD14GHZ, default is ""
-loc LOCNAME : specify location/study name, required
-F FILE: specify output file, default is magic_measurements.txt
-Fsa FILE: specify er_samples formatted file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-sit Site_name : specify site name for this specimen
-unc measurement units are uncalibrated (default is uAm^2)
-B PHI THETA: dc lab field phi, theta, default is 0, 90
-ncn NCON: specify naming convention - required if -sit not specified
Sample naming convention:
do not use if -sit option used!
[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
[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.
"""
# initialize some stuff
version_num = pmag.get_version()
noave = 0
methcode, instcode = "", ""
phi, theta, peakfield, labfield = 0, 0, 0, 0
pMRM, MD, samp_con, Z, site = 0, 0, "6", "", ""
er_location_name = ""
citation = "This study"
args = sys.argv
methcode = "LP-NO" # NRM
specnum, measnum = 1, 1
powt_max = 0
ErSamps, Samps = [], []
#
# get command line arguments
#
dirpath = "."
meas_file, samp_file = dirpath + "/magic_measurements.txt", dirpath + "/er_samples.txt"
user = ""
unc = 0
if "-WD" in args:
ind = args.index("-WD")
dirpath = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if "-ins" in args:
ind = args.index("-ins")
instcode = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = dirpath + "/" + args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
samp_file = dirpath + "/" + samp_file
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
print "sample information will be appended to new er_samples.txt file"
except:
print "er_samples.txt file does not exist"
print "sample information will be stored in new er_samples.txt file"
if "-f" in args:
ind = args.index("-f")
magfile = args[ind + 1]
magfile = dirpath + "/" + magfile
try:
input = open(magfile, "rU")
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-B" in args:
ind = args.index("-B")
phi = args[ind + 1]
theta = args[ind + 2]
else:
phi, theta = "0.", "90."
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-unc" in args:
unc = 1
if "-sit" in args:
ind = args.index("-sit")
site = args[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if samp_con == "6" and site == "":
print "you must either specify a naming convention, or a site name"
print main.__doc__
sys.exit()
MagRecs = []
if len(ErSamps) > 1:
for samp in ErSamps:
if samp["er_sample_name"] not in Samps:
Samps.append(samp["er_sample_name"])
Data = input.readlines()
if 1: # never mind
for line in Data:
if len(line) > 1:
rec = line.split(",")
MagRec = {}
MagRec["er_citation_names"] = "This study"
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"] = ""
MagRec["treatment_dc_field_theta"] = ""
MagRec["treatment_mw_integral"] = ""
meas_type = "LT-NO"
MagRec["er_specimen_name"] = rec[0][1:-1]
MagRec["er_location_name"] = er_location_name
if specnum != 0:
MagRec["er_sample_name"] = rec[0][1:-1][:specnum]
else:
MagRec["er_sample_name"] = rec[0][1:-1]
if site == "":
site = pmag.parse_site(MagRec["er_sample_name"], samp_con, Z)
MagRec["er_site_name"] = site
MagRec["treatment_mw_power"] = rec[2]
MagRec["treatment_mw_time"] = rec[3]
powt = int(float(MagRec["treatment_mw_power"]) * (float(MagRec["treatment_mw_time"])))
MagRec["treatment_mw_energy"] = "%7.1f" % (powt)
if powt > powt_max:
powt_max = powt
treat = rec[1].strip('"').upper()
if treat == "Z": # in zero field
meas_type = "LT-M-Z" # as opposed to LT-MV-Z
if powt < powt_max:
meas_type = "LT-PMRM-Z"
elif treat == "A": # in zero field
meas_type = "LT-M-I" # as opposed to LT-MV-I
labfield = float(rec[10]) * 1e-6 # assuming uT, convert to T
MagRec["treatment_dc_field"] = "%8.3e" % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"] = phi # labfield phi
MagRec["treatment_dc_field_theta"] = theta # labfield theta
if powt < powt_max:
meas_type = "LT-PMRM-I"
if len(rec) > 10:
MagRec["treatment_mw_integral"] = rec[10]
if unc == 0:
MagRec["measurement_magn_moment"] = "%10.3e" % (float(rec[4]) * 1e-6) # moment in Am^2 (from uAm^2)
if unc == 1:
MagRec["measurement_magnitude"] = rec[4] # uncalibrated moment
cart = []
cart.append(float(rec[7]))
cart.append(float(rec[8]))
cart.append(float(rec[9]))
dir = pmag.cart2dir(cart)
MagRec["measurement_dec"] = "%9.3f" % (dir[0])
MagRec["measurement_inc"] = "%9.3f" % (dir[1])
MagRec["magic_instrument_codes"] = instcode
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "%i" % (measnum)
MagRec["magic_experiment_name"] = MagRec["er_specimen_name"] + ":" + methcode
measnum += 1
MagRecs.append(MagRec)
if MagRec["er_sample_name"] not in Samps: # add this puppy to the list in er_samples.txt
Samps.append(MagRec["er_sample_name"])
ErSamp = {}
ErSamp["er_sample_name"] = Samps[-1]
ErSamp["er_location_name"] = MagRec["er_location_name"]
ErSamp["er_site_name"] = site
ErSamp["er_citation_names"] = "This study"
gdec = float(rec[5])
ginc = float(rec[6])
az, pl = pmag.get_azpl(dir[0], dir[1], gdec, ginc)
ErSamp["sample_azimuth"] = "%7.1f" % az
ErSamp["sample_dip"] = "%7.1f" % pl
ErSamps.append(ErSamp)
MagOuts = pmag.mw_measurements_methods(MagRecs)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "measurements put in ", meas_file
pmag.magic_write(samp_file, ErSamps, "er_samples")
print "sample names put in ", samp_file
def main():
"""
NAME
mag_magic.py
DESCRIPTION
converts SIO .mag format files to magic_measurements format files
SYNTAX
mag_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
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-Fsa: specify output er_samples file, default is NONE (only for LDGO formatted files)
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
S: Shaw method
T: thermal including thellier but not trm acquisition
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
-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
-FT [SIO,LDGO] : file type. default is SIO (.mag file format)
-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
[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 - Lectures in Paleomagnetism, 2007)
TRM:
XXX.YYY XXX is temperature step of total TRM
YYY is dc field in microtesla
Shaw:
XXX.YY XXX is AF field
YY=00 is AF of NRM
YY=01 is AF of ARM1
YY=02 is AF of TRM
YY=03 is AF of ARM2
specify temperature and field of Total TRM step on command line
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...)
Format of LDGO files:
SPEC TREAT INST CSD Intensity CDECL CINCL [GDECL GINCL BDECL BINCL SUSC ]
"""
# initialize some stuff
infile_type="mag"
noave=0
methcode,inst="",""
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]
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
fmt='old'
syn=0
synfile='er_synthetics.txt'
samp_file,ErSamps='',[]
trm=0
irm=0
specnum=0
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if "-h" in args:
print main.__doc__
sys.exit()
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 '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
print 'sample information will be appended to new er_samples.txt file'
except:
print 'sample information will be stored in new er_samples.txt file'
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
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 specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
Samps,file_type=pmag.magic_read(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 '-FT' in args:
ind=args.index("-FT")
FT=args[ind+1]
if FT=="LDGO":infile_type="ldgo" # default is "mag"
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
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"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_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 demag=="T" and "ANI" in codes:
methcode="LP-AN-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 infile_type=="mag":
for line in input.readlines():
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 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)
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[2]=='mT':
if methcode=="LP-IRM":
labfield=float(code1[3])*1e-3
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)
else:
demag="AF"
labfield=float(code1[3])*1e-6
if code1[4]=='microT' and labfield!=0.:
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.:
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 "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
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:
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 rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
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
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(0)
if labfield!=0: print "Warning - inconsistency in mag file with lab field - overriding file with 0"
else:
meas_type="LT-AF-I"
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=="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"
else:
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
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'
MagRec["er_specimen_name"],meas_type
MagRecs.append(MagRec)
elif infile_type=="ldgo":
#
# find start of data:
#
Samps=[] # keeps track of sample orientations
DIspec=[]
Data,k=input.readlines(),0
for k in range(len(Data)):
rec=Data[k].split()
if rec[0][0]=="_" or rec[0][0:2]=="!_":
break
start=k+1
for k in range(start,len(Data)):
rec=Data[k].split()
if len(rec)>0:
MagRec={}
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"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
MagRec["er_site_name"]=MagRec['er_sample_name'][0:-2]
MagRec["er_location_name"]=er_location_name
MagRec["measurement_csd"]=rec[3]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[4])*1e-7) # moment in Am^2 (from 10^-4 emu)
#
if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
cdec,cinc=float(rec[5]),float(rec[6])
gdec,ginc=float(rec[7]),float(rec[8])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
bdec,binc=float(rec[9]),float(rec[10])
if rec[7]!=rec[9] and rec[6]!=rec[8]:
dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
else:
dipdir,dip=0,0
ErSampRec={}
ErSampRec['er_location_name']=MagRec['er_location_name']
ErSampRec['er_sample_name']=MagRec['er_sample_name']
ErSampRec['er_site_name']=MagRec['er_site_name']
ErSampRec['sample_azimuth']='%7.1f'%(az)
ErSampRec['sample_dip']='%7.1f'%(pl)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in ldeo file'
ErSampRec['magic_method_codes']='SO-REC'
ErSamps.append(ErSampRec)
Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"]=rec[5]
MagRec["measurement_inc"]=rec[6]
MagRec["magic_instrument_codes"]=rec[2]
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
else:
meas_type="LT-AF-I"
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":
if rec[1][0]==".":rec[1]="0"+rec[1]
treat=rec[1].split('.')
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(rec[1])+273.) # temp in kelvin
meas_type="LT-T-Z"
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:
meas_type="LT-T-I" # trm acquisition experiment
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
if samp_file!="":
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "sample orientations put in ",samp_file
if len(SynRecs)>0:
pmag.magic_write(synfile,SynRecs,'er_synthetics')
print "synthetics put in ",synfile