def main(command_line=True, **kwargs):
"""
NAME
jr6_magic.py
DESCRIPTION
converts JR6 format files to magic_measurements format files
SYNTAX
jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-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
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
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.
INPUT
JR6 .txt format file
"""
# initialize some stuff
noave=0
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
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]
#try:
# open(samp_file,'r')
# 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 = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args:
noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False
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")
return False
else:
Z=samp_con.split("-")[1]
samp_con="7"
ErSampRec,ErSiteRec={},{}
# parse data
data=open(mag_file,'r')
line=data.readline()
line=data.readline()
line=data.readline()
while line !='':
parsedLine=line.split()
sampleName=parsedLine[0]
demagLevel=parsedLine[2]
date=parsedLine[3]
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
parsedLine=line.split()
specimenAngleDec=parsedLine[1]
specimenAngleInc=parsedLine[2]
while parsedLine[0] != 'MEAN' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
Mx=parsedLine[1]
My=parsedLine[2]
Mz=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
splitExp = parsedLine[2].split('A')
intensityStr=parsedLine[1] + splitExp[0]
intensity = float(intensityStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr=''
if len(parsedLine) == 6: #normal line
precisionStr=parsedLine[5][0:-1]
else:
precisionStr=parsedLine[4][0:-1]
precisionPer = float(precisionStr)
precision=intensity*precisionPer/100
while parsedLine[0] != 'SPEC.' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
specimenDec=parsedLine[2]
specimenInc=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
geographicDec=parsedLine[1]
geographicInc=parsedLine[2]
# Add data to various MagIC data tables.
er_specimen_name = sampleName
if specnum!=0:
er_sample_name=er_specimen_name[:specnum]
else:
er_sample_name=er_specimen_name
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# check sample list(SampOuts) to see if sample already exists in list before adding new sample info
sampleFlag=0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == er_sample_name:
sampleFlag=1
break
if sampleFlag == 0:
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['sample_azimuth']=specimenAngleDec
ErSampRec['sample_dip']=specimenAngleInc
ErSampRec['magic_method_codes']=meth_code
ErSampRec['er_location_name']=er_location_name
ErSampRec['er_site_name']=er_site_name
ErSampRec['er_citation_names']='This study'
SampOuts.append(ErSampRec.copy())
MagRec={}
MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_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["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
MagRec["treatment_ac_field"]='0'
if demagLevel == 'NRM':
meas_type="LT-NO"
elif demagLevel[0] == 'A':
meas_type="LT-AF-Z"
treat=float(demagLevel[1:])
MagRec["treatment_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:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown")
return False
# X=[float(Mx),float(My),float(Mz)]
# Vec=pmag.cart2dir(X)
# MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MagRec["measurement_magn_moment"]=str(intensity*0.025*0.025*0.025) # Am^2 assume 2.5cm cube sample
MagRec["measurement_magn_volume"]=intensityStr
MagRec["measurement_dec"]=specimenDec
MagRec["measurement_inc"]=specimenInc
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
#read lines till end of record
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
# read all the rest of the special characters. Some data files not consistantly formatted.
while (len(line) <=3 and line!=''):
line=data.readline()
#end of data while loop
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(samp_file,SampOuts,'er_samples')
print("sample orientations put in ",samp_file)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print("results put in ",meas_file)
return True
def main(command_line=True, **kwargs):
"""
NAME
_2g_bin_magic.py
DESCRIPTION
takes the binary 2g format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2g_bin_magic.py [command line options]
OPTIONS
-f FILE: specify input 2g (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sites.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
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 = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
mag_file = ''
specnum=0
ub_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","3","1","magic_measurements.txt"
pos_file,site_file="","er_sites.txt"
noave=1
args=sys.argv
bed_dip,bed_dip_dir="",""
samp_con,Z,average_bedding="2",1,"0"
meths='FS-FD'
sclass,lithology,_type="","",""
user,inst="",""
DecCorr=0.
location_name="unknown"
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
gmeths=""
#
#
dir_path='.'
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in args:
print main.__doc__
return False
if "-f" in args:
ind=args.index("-f")
mag_file=sys.argv[ind+1]
if "-fpos" in args:
ind=args.index("-fpos")
pos_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
meas_file=sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-Fsi" in args:
ind=args.index("-Fsi")
site_file=sys.argv[ind+1]
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-mcd" in args:
ind=args.index("-mcd")
gmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-a" in args:
noave=0
#
ID = False
if '-ID' in args:
ind = args.index('-ID')
ID = args[ind+1]
#
if not command_line:
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
pos_file = kwargs.get('pos_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', '')
location_name = kwargs.get('location_name', '')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 1) # default is DO average
ID = kwargs.get('ID', '')
# format and fix variables acquired from command line args or input with **kwargs
if specnum!=0:specnum=-specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "option [4] must be in form 4-Z where Z is an integer"
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"
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 "6" in samp_con:
try:
Samps,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
except:
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if file_type == 'bad_file':
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if not mag_file:
print "mag file is required input"
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = output_dir_path+'/'+samp_file
site_file = output_dir_path+'/'+site_file
meas_file= output_dir_path+'/'+meas_file
samplist=[]
try:
Samps,file_type=pmag.magic_read(samp_file)
for samp in Samps:
if samp['er_sample_name'] not in samplist: samplist.append(samp['er_sample_name'])
except:
Samps=[]
MagRecs=[]
try:
f=open(mag_file,'rU')
input=f.read()
f.close()
except Exception as ex:
print 'ex', ex
print "bad mag file"
return False, "bad mag file"
firstline,date=1,""
d=input.split('\xcd')
for line in d:
rec=line.split('\x00')
if firstline==1:
firstline=0
spec,vol="",1
for c in line[15:23]:
if c!='\x00':spec=spec+c
# check for bad sample name
test=spec.split('.')
date=""
if len(test)>1:
spec=test[0]
kk=24
while line[kk]!='\x01' and line[kk]!='\x00':
kk+=1
vcc=line[24:kk]
el=10
while rec[el].strip()!='':el+=1
date,comments=rec[el+7],[]
else:
el=9
while rec[el]!='\x01':el+=1
vcc,date,comments=rec[el-3],rec[el+7],[]
specname=spec.lower()
print 'importing ',specname
el+=8
while rec[el].isdigit()==False:
comments.append(rec[el])
el+=1
while rec[el]=="":el+=1
az=float(rec[el])
el+=1
while rec[el]=="":el+=1
pl=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip_dir=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip=float(rec[el])
el+=1
while rec[el]=="":el+=1
if rec[el]=='\x01':
bed_dip=180.-bed_dip
el+=1
while rec[el]=="":el+=1
fold_az=float(rec[el])
el+=1
while rec[el]=="":el+=1
fold_pl=rec[el]
el+=1
while rec[el]=="":el+=1
if rec[el]!="" and rec[el]!='\x02' and rec[el]!='\x01':
deccorr=float(rec[el])
az+=deccorr
bed_dip_dir+=deccorr
fold_az+=deccorr
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
if az>=360.:az=az-360.
if fold_az>=360.:fold_az=fold_az-360.
else:
deccorr=0
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
SampRec={}
SampRec["er_sample_name"]=sample
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"]='%7.1f'%(bed_dip)
SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
if vcc.strip()!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SampRec["sample_volume"]='%10.3e'%(vol) #
SampRec["sample_class"]=sclass
SampRec["sample_lithology"]=lithology
SampRec["sample_type"]=_type
SampRec["sample_declination_correction"]='%7.1f'%(deccorr)
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths=""
for meth in methods:meths=meths+meth+":"
meths=meths[:-1]
SampRec["magic_method_codes"]=meths
if int(samp_con)<6 or int(samp_con) == 7:
site=pmag.parse_site(SampRec["er_sample_name"],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
elif len(Samps)>1:
site,location="",""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site=samp["er_site_name"]
location=samp["er_location_name"]
break
SampRec["er_location_name"]=samp["er_location_name"]
SampRec["er_site_name"]=samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
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"]=specname
MagRec["er_sample_name"]=SampRec['er_sample_name']
MagRec["er_site_name"]=SampRec['er_site_name']
MagRec["er_location_name"]=location_name
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MagRec["measurement_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MagRec["measurement_inc"]=rec[el]
cinc=float(rec[el])
el+=1
while rec[el]=="":el+=1
gdec=rec[el]
el+=1
while rec[el]=="":el+=1
ginc=rec[el]
el=skip(2,el,rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MagRec["measurement_sd_x"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MagRec["measurement_sd_y"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MagRec["measurement_sd_z"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MagRec["measurement_positions"]=rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (float(treat[:-1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
MagOuts, keylist = pmag.fillkeys(MagOuts)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "Measurements put in ",meas_file
SampsOut,sampkeys=pmag.fillkeys(Samps)
pmag.magic_write(samp_file,SampsOut,"er_samples")
Sites=[]
for samp in Samps:
SiteRec={}
SiteRec['er_site_name']=samp['er_site_name']
SiteRec['er_location_name']=samp['er_location_name']
SiteRec['site_definition']='s'
SiteRec['er_citation_names']='This study'
if 'sample_class' in samp.keys():SiteRec['site_class']=samp['sample_class']
if 'sample_lithology' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_type' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_lat' in samp.keys():
SiteRec['site_lat']=samp['sample_lat']
else:
SiteRec['site_lat']="-999"
if 'sample_lon' in samp.keys():
SiteRec['site_lon']=samp['sample_lon']
else:
SiteRec['site_lon']="-999"
if 'sample_height' in samp.keys():SiteRec['site_height']=samp['sample_height']
Sites.append(SiteRec)
pmag.magic_write(site_file,Sites,'er_sites')
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
jr6_jr6_magic.py
DESCRIPTION
converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
jr6_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-JR IODP samples measured on the JOIDES RESOLUTION
-v NUM : specify the volume in cc of the sample, default 2.5^3cc
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.
INPUT
JR6 .jr6 format file
"""
# initialize some stuff
noave=0
#volume=2.5**3 #default volume is a 2.5cm cube
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=1
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
user=""
mag_file=""
dir_path='.'
MagRecs=[]
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
tmp_file= "fixed.jr6"
meth_code,JR="",0
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
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]
#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 = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if "-JR" in args:
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
JR=1
samp_con='5'
if "-v" in args:
ind=args.index("-v")
volume=float(args[ind+1])*1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
JR = kwargs.get('JR', 0)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
samp_con='5'
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
tmp_file = output_dir_path+"/" + tmp_file
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "option [4] must be in form 4-Z where Z is an integer"
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"
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
ErSampRec,ErSiteRec={},{}
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data=open(mag_file, 'rU')
tmp_data=open(tmp_file, 'w')
line=pre_data.readline()
while line !='':
line=line.replace('-',' -')
#print "line=", line
tmp_data.write(line)
line=pre_data.readline()
tmp_data.close()
pre_data.close()
data=pd.read_csv(tmp_file, delim_whitespace=True,header=None)
if JR==0: #
data.columns=['er_specimen_name','step','x','y','z','expon','sample_azimuth','sample_dip', 'sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],data['z']]).transpose()
else: # measured on the Joides Resolution JR6
data.columns=['er_specimen_name','step','negz','y','x','expon','sample_azimuth','sample_dip', 'sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_moment']=dir[2]*(10.0**data['expon'])*volume # the data are in A/m - this converts to Am^2
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['sample_dip']=-data['sample_dip']
DGEOs,IGEOs=[],[]
for ind in range(len(data)):
dgeo,igeo=pmag.dogeo(data.ix[ind]['measurement_dec'],data.ix[ind]['measurement_inc'],data.ix[ind]['sample_azimuth'],data.ix[ind]['sample_dip'])
DGEOs.append(dgeo)
IGEOs.append(igeo)
data['specimen_dec']=DGEOs
data['specimen_inc']=IGEOs
data['specimen_tilt']='1'
if specnum!=0:
data['er_sample_name']=data['er_specimen_name'][:specnum]
else:
data['er_sample_name']=data['er_specimen_name']
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
data['er_site_name']=pmag.parse_site(data['er_sample_name'],samp_con,Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# Configure the er_sample table
for rowNum, row in data.iterrows():
sampleFlag=0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == row['er_sample_name']:
sampleFlag=1
break
if sampleFlag == 0:
ErSampRec['er_sample_name']=row['er_sample_name']
ErSampRec['sample_azimuth']=str(row['sample_azimuth'])
ErSampRec['sample_dip']=str(row['sample_dip'])
ErSampRec['magic_method_codes']=meth_code
ErSampRec['er_location_name']=er_location_name
ErSampRec['er_site_name']=row['er_site_name']
ErSampRec['er_citation_names']='This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec={}
# MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=row['er_site_name']
MagRec['er_sample_name']=row['er_sample_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["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=row['er_specimen_name']
MagRec["treatment_ac_field"]='0'
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else: # need to add IRM, and ARM options
print "measurement type unknown", row['step']
return False, "measurement type unknown"
MagRec["measurement_magn_moment"]=str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]=str(row['measurement_dec'])
MagRec["measurement_inc"]=str(row['measurement_inc'])
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
print "exit!"
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
pmd_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
pmd_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-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
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
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.
INPUT
PMD format files
"""
# initialize some stuff
noave=0
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
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]
#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 = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention 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"
if "7" in samp_con:
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"
# parse data
data=open(mag_file,'rU').readlines() # read in data from file
comment=data[0]
line=data[1].strip()
line=line.replace("=","= ") # make finding orientations easier
rec=line.split() # read in sample orientation, etc.
er_specimen_name=rec[0]
ErSampRec,ErSiteRec={},{} # make a sample record
if specnum!=0:
er_sample_name=rec[0][:specnum]
else:
er_sample_name=rec[0]
if len(ErSamps)>0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name']==er_sample_name:
ErSampRec=samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con)<6:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
else:
if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampREc['er_location_name']
az_ind=rec.index('a=')+1
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['er_sample_description']=comment
ErSampRec['sample_azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
ErSampRec['sample_dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
ErSampRec['sample_bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
ErSampRec['sample_bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
ErSampRec['magic_method_codes']=meth_code
if 'er_location_name' not in ErSampRec.keys():ErSampRec['er_location_name']=er_location_name
if 'er_site_name' not in ErSampRec.keys():ErSampRec['er_site_name']=er_site_name
if 'er_citation_names' not in ErSampRec.keys():ErSampRec['er_citation_names']='This study'
if 'magic_method_codes' not in ErSampRec.keys():ErSampRec['magic_method_codes']='SO-NO'
SampOuts.append(ErSampRec)
for k in range(3,len(data)): # read in data
line=data[k]
rec=line.split()
if len(rec)>1: # skip blank lines at bottom
MagRec={}
MagRec['measurement_description']='Date: '+date+' '+time
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_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["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
if rec[0]=='NRM':
meas_type="LT-NO"
elif rec[0][0]=='M' or rec[0][0]=='H':
meas_type="LT-AF-Z"
elif rec[0][0]=='T':
meas_type="LT-T-Z"
else:
print "measurement type unknown"
return False, "measurement type unknown"
X=[float(rec[1]),float(rec[2]),float(rec[3])]
Vec=pmag.cart2dir(X)
MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"]='%7.1f'%(Vec[0])
MagRec["measurement_inc"]='%7.1f'%(Vec[1])
MagRec["treatment_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
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,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
old_iodp_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
old_iodp_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave=0
volume=2.5**3 #default volume is a 2.5cm cube
inst=""
samp_con,Z='5',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
version_num=pmag.get_version()
dir_path='.'
MagRecs=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
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]
if samp_file[0]!='/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
except:
print samp_file,' not found: '
print ' download csv file and import to MagIC with iodp_samples_magic.py'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args:
noave=1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print "You must provide an IODP_jr6 format file"
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(os.path.join(input_dir_path, mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(magfile)
if not os.path.exists(samp_file):
print 'samp_file', samp_file
print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
#os.rename('temp.txt', mag_file)
#data = open(mag_file, 'rU').readlines()
data=pd.read_csv(temp, delim_whitespace=True,header=None)
os.remove(temp)
samples,filetype = pmag.magic_read(samp_file)
data.columns=['specname','step','negz','y','x','expon','sample_azimuth','sample_dip','sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['measurement_flag']='g'
data['measurement_standard']='u'
data['measurement_number']='1'
data['measurement_temp']='273'
data['er_location_name']=er_location_name
for rowNum, row in data.iterrows():
MagRec={}
spec_text_id=row['specname'].split('_')[1]
SampRecs=pmag.get_dictitem(samples,'er_sample_alternatives',spec_text_id,'has') # retrieve sample record for this specimen
if len(SampRecs)>0: # found one
MagRec['er_specimen_name']=SampRecs[0]['er_sample_name']
MagRec['er_sample_name']=MagRec['er_specimen_name']
MagRec['er_site_name']=MagRec['er_specimen_name']
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["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["treatment_ac_field"]='0'
volume=float(SampRecs[0]['sample_volume'])
moment=row['measurement_magn_volume'] * volume
MagRec["measurement_magn_moment"]=str(moment)
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]='%7.1f'%(row['measurement_dec'])
MagRec["measurement_inc"]='%7.1f'%(row['measurement_inc'])
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:3]=='ARM': #
meas_type="LT-AF-I"
treat=float(row['step'][3:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field
MagRec["measurement_description"]='Assumed DC field - actual unknown'
elif row['step'][0:3]=='IRM': #
meas_type="LT-IRM"
treat=float(row['step'][3:])
MagRec["treatment_dc_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
else:
print 'unknown treatment type for ',row
return False, 'unknown treatment type for ',row
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
else:
print 'sample name not found: ',row['specname']
MagOuts=pmag.measurements_methods(MagRecs,noave)
file_created, error_message = pmag.magic_write(meas_file,MagOuts,'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main():
"""
NAME
odp_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
odp_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-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
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num = pmag.get_version()
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
ErSpecs, ErSamps, ErSites, ErLocs, ErCits = [], [], [], [], []
MagRecs = []
citation = "This study"
dir_path, demag = '.', 'NRM'
args = sys.argv
noave = 0
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-A" in args: noave = 1
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = dir_path + '/' + args[ind + 1]
ErSamps, file_type = pmag.magic_read(samp_file)
else:
samp_file = dir_path + '/' + samp_file
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 = 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 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
spec_file = dir_path + '/' + spec_file
site_file = dir_path + '/' + site_file
meas_file = dir_path + '/' + meas_file
filelist = os.listdir(dir_path) # read in list of files to import
specimens, samples, sites = [], [], []
MagRecs, SpecRecs, SampRecs = [], [], []
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower() == 'dsc':
print('processing: ', file)
MagRec, SpecRec, SampRec = {}, {}, {}
treatment_type, treatment_value, user = "", "", ""
inst = "ODP-SRM"
input = open(dir_path + '/' + file, 'r').readlines()
IDs = file.split('_') # splits on underscores
pieces = IDs[0].split('-')
expedition = pieces[0]
location = pieces[1]
if file[0] != '_':
while len(pieces[2]) < 4:
pieces[2] = '0' + pieces[2] # pad core to be 3 characters
specimen = ""
else:
specimen = "test"
for piece in pieces:
specimen = specimen + piece + '-'
specimen = specimen[:-1]
alt_spec = IDs[
1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name'] = expedition
SpecRec['er_location_name'] = location
SpecRec['er_site_name'] = specimen
SpecRec['er_sample_name'] = specimen
SpecRec['er_citation_names'] = citation
for key in list(SpecRec.keys()):
SampRec[key] = SpecRec[key]
SampRec['sample_azimuth'] = '0'
SampRec['sample_dip'] = '0'
SampRec['magic_method_codes'] = 'FS-C-DRILL-IODP:SP-SS-C:SO-V'
SpecRec['er_specimen_name'] = specimen
SampRec['er_specimen_names'] = specimen
for key in list(SpecRec.keys()):
MagRec[key] = SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names'] = user
MagRec['magic_method_codes'] = 'LT-NO'
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'
MagRec["measurement_flag"] = 'g' # assume all data are "good"
MagRec["measurement_standard"] = 'u' # assume all data are "good"
MagRec["measurement_csd"] = '' # set csd to blank
SpecRec['er_specimen_alternatives'] = alt_spec
vol = 7e-6 # assume 7 cc samples
datestamp = input[1].split() # date time is second line of file
mmddyy = datestamp[0].split('/') # break into month day year
date = mmddyy[2] + ':' + mmddyy[0] + ":" + mmddyy[
1] + ':' + datestamp[1]
MagRec["measurement_date"] = date
for k in range(len(input)):
fields = input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type = "AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst = inst + ':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type = "ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst = inst + ':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type = "IRM"
if "treatment_value" in fields[0]:
values = fields[1].split(',')
value = values[0]
if value != " \n":
if treatment_type == "AF":
treatment_value = float(value) * 1e-3
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
elif treatment_type == "IRM":
treatment_value = float(value) * 1e-3
MagRec["treatment_dc_field"] = '%8.3e' % (
treatment_value) # IRM treat mT => T
if treatment_type == "ARM":
treatment_value = float(value) * 1e-3
dc_value = float(values[1]) * 1e-3
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"] = '%8.3e' % (
dc_value) # DC mT => T
if 'user' in fields[0]:
user = fields[-1]
MagRec["er_analyst_mail_names"] = user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"] = fields[-1]
MagRec[
"measurement_standard"] = 'u' # assume all data are "good"
if 'sample_area' in fields[0]:
vol = float(
fields[1]
) * 1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids'] = fields[
1] # run number is the LIMS measurement number
MagRec['external_database_names'] = 'LIMS'
if input[k][0:7] == '<MULTI>':
rec = input[k + 1].split(',') # list of data
for item in rec:
items = item.split('=')
if items[0].strip(
) == 'demag_level' and treatment_value == "":
treat = float(items[1])
if treat != 0:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':ODP-SRM-AF'
MagRec[
"treatment_ac_field"] = treat * 1e-3 # AF demag in treat mT => T
if items[0].strip() == 'inclination_w_tray_w_bkgrd':
MagRec['measurement_inc'] = items[1]
if items[0].strip() == 'declination_w_tray_w_bkgrd':
MagRec['measurement_dec'] = items[1]
if items[0].strip() == 'intensity_w_tray_w_bkgrd':
MagRec['measurement_magn_moment'] = '%8.3e' % (
float(items[1]) * vol
) # convert intensity from A/m to Am^2 using vol
if items[0].strip() == 'x_stdev':
MagRec['measurement_x_sd'] = items[1]
if items[0].strip() == 'y_stdev':
MagRec['measurement_y_sd'] = items[1]
if items[0].strip() == 'z_stdev':
MagRec['measurement_sd_z'] = items[1]
MagRec['magic_instrument_codes'] = inst
MagRec['measurement_number'] = '1'
MagRec['measurement_positions'] = ''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts = pmag.sort_diclist(MagRecs, 'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"] = '%8.3e' % (MagRec["treatment_ac_field"]
) # convert to string
pmag.magic_write(spec_file, SpecRecs, 'er_specimens')
if len(SampRecs) > 0:
SampOut, keys = pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file, SampOut, 'er_samples')
print('samples stored in ', samp_file)
pmag.magic_write(samp_file, SampRecs, 'er_samples')
print('specimens stored in ', spec_file)
Fixed = pmag.measurements_methods(MagOuts, noave)
pmag.magic_write(meas_file, Fixed, 'magic_measurements')
print('data stored in ', meas_file)
def main(command_line=True, **kwargs):
"""
NAME
bgc_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
bgc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume in cc of the sample, default 2.5^3cc. Will use vol in data file if volume!=0 in file.
INPUT
BGC paleomag format file
"""
# initialize some stuff
noave = 0
volume = 0.025**3 #default volume is a 2.5cm cube
#inst=""
#samp_con,Z='1',""
#missing=1
#demag="N"
er_location_name = "unknown"
er_site_name = "unknown"
#citation='This study'
args = sys.argv
meth_code = "LP-NO"
#specnum=1
version_num = pmag.get_version()
mag_file = ""
dir_path = '.'
MagRecs = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
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]
#try:
# open(samp_file,'r')
# 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 = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind + 1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
#samp_con='5'
if "-v" in args:
ind = args.index("-v")
volume = float(
args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
er_location_name = kwargs.get('er_location_name', '')
er_site_name = kwargs.get('er_site_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
# format variables
if not mag_file:
return False, 'You must provide a BCG format file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
sample_name = line_items[2]
sample_name = sample_name.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
sample_azimuth = float(line_items[1])
sample_dip = float(line_items[2])
sample_bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
sample_lon = line_items[5]
sample_lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['measurement_dec'] = direction[0]
data['measurement_inc'] = direction[1]
data['measurement_magn_moment'] = old_div(
direction[2], 1000) # the data are in EMU - this converts to Am^2
data['measurement_magn_volume'] = old_div(
(old_div(direction[2], 1000)), volume) # EMU - data converted to A/m
# Configure the er_sample table
ErSampRec['er_sample_name'] = sample_name
ErSampRec['sample_azimuth'] = sample_azimuth
ErSampRec['sample_dip'] = sample_dip
ErSampRec['sample_bed_dip_direction'] = sample_bed_azimuth
ErSampRec['sample_bed_dip'] = sample_bed_dip
ErSampRec['sample_lat'] = sample_lat
ErSampRec['sample_lon'] = sample_lon
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
MagRec['measurement_description'] = 'Date: ' + str(
row['Date']) + ' Time: ' + str(row['Time'])
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_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["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = rowNum
MagRec["er_specimen_name"] = sample_name
MagRec["treatment_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ",
rowNum)
MagRec["measurement_magn_moment"] = str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"] = str(row['measurement_magn_volume'])
MagRec["measurement_dec"] = str(row['measurement_dec'])
MagRec["measurement_inc"] = str(row['measurement_inc'])
MagRec['magic_method_codes'] = meas_type
MagRec['measurement_csd'] = '0.0' # added due to magic.write error
MagRec['measurement_positions'] = '1' # added due to magic.write error
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print("sample orientations put in ", samp_file)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-WD Working Directory: output directory where files are going to go
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-dc B PHI THETA: dc lab field (in microTesla), phi,and theta must be input as a tuple "(DC,PHI,THETA)". If not input user will be asked for values, this is advantagious if there are differing dc fields between steps or specimens. Note: this currently only works with the decimal IZZI naming convetion (XXX.0,1,2 where XXX is the treatment temperature and 0 is a zero field step, 1 is in field, and 2 is a pTRM check). All other steps are hardcoded dc_field = 0.
INPUT
Best to put separate experiments in separate files (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
NOTES:
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: default] 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 = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] or [email protected] for help.
"""
#
# 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
#
#initialize variables
norm='cc'
samp_con,Z='3',1
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MeasRecs=[]
specnum,units,locname=0,"1","unknown"
citation="This study"
dir_path='.'
args=sys.argv
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
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 '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-Fsi' in args: # LORI addition
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-loc' in args:
ind=args.index("-loc")
locname=args[ind+1]
if '-mcd' in args:
ind=args.index("-mcd")
methods=args[ind+1]
else:
methods='SO-MAG'
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if '-n' in args:
ind=args.index("-n")
norm=args[ind+1]
if "-A" in args:
avg=1
else:
avg=0
if '-dc' in args:
ind=args.index('-dc')
DC_FIELD,DC_PHI,DC_THETA=list(map(float,args[ind+1].strip('( ) [ ]').split(',')))
DC_FIELD *= 1e-6
yn=''
GET_DC_PARAMS=False
else: GET_DC_PARAMS,DC_FIELD,DC_PHI,DC_THETA,yn=True,0,0,-90,''
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")
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 "7" in samp_con:
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"
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = os.path.split(magfile)[0]
output_dir_path = dir_path
# LJ
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path', os.path.split(magfile)[0])
output_dir_path = dir_path
DC_FIELD,DC_PHI,DC_THETA = list(map(float, kwargs.get('dc_params', (0,0,-90))))
DC_FIELD *= 1e-6
yn = ''
if DC_FIELD==0 and DC_PHI==0 and DC_THETA==-90: GET_DC_PARAMS=True
else: GET_DC_PARAMS=False
# done with module-specific stuff
# formatting and checking variables
if "4" in samp_con:
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 "7" in samp_con:
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"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file= os.path.join(output_dir_path, meas_file)
FIRST_GET_DC=True
try:
with open(magfile,'r') as file_input:
File = file_input.readlines()
except Exception as ex:
print("bad sam file name: ", magfile)
return False, "bad sam file name"
if len(File) == 1: File = File[0].split('\r'); File = [x+"\r\n" for x in File]
sids,ln,format=[],0,'CIT'
formats=['CIT','2G','APP','JRA']
if File[ln].strip()=='CIT': ln+=1
ErLocRec={}
ErLocRec["er_location_name"]=locname
ErLocRec["er_citation_names"]=citation
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print(comment)
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
ErLocRec["location_begin_lat"]=site_lat
ErLocRec["location_begin_lon"]=site_lon
ErLocRec["location_end_lat"]=site_lat
ErLocRec["location_end_lon"]=site_lon
ErLocs.append(ErLocRec)
try: Cdec=float(line[2])
except ValueError: pdb.set_trace()
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
if rec == []: continue
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec,ErSampRec,ErSiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
ErSpecRec['er_specimen_name']=specimen
ErSpecRec['er_sample_name']=sample
ErSpecRec['er_site_name']=site
ErSpecRec['er_location_name']=locname
ErSpecRec['er_citation_names']=citation
ErSampRec['er_sample_name']=sample
ErSampRec['er_site_name']=site
ErSampRec['er_location_name']=locname
ErSampRec['er_citation_names']=citation
ErSampRec['magic_method_codes']=methods
ErSampRec['sample_declination_correction']='%7.1f'%(Cdec)
ErSiteRec['er_site_name']=site
ErSiteRec['er_location_name']=locname
ErSiteRec['er_citation_names']=citation
ErSiteRec['site_lat']=site_lat
ErSiteRec['site_lon']=site_lon
with open(os.path.join(input_dir_path,specimen),'r') as finput:
Lines = list(finput.readlines())
comment = ""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
vol=float(info[-1])
if vol!=1.0:
if norm=='cc':units="1"
if norm=='m3':units="2"
ErSpecRec['specimen_weight']=""
if units=="1" or "":
ErSpecRec['specimen_volume']='%10.3e'%(vol*1e-6)
else:
ErSpecRec['specimen_volume']='%10.3e'%(vol)
else:
if norm=='cc':units="1"
if norm=='m3':units="2"
ErSpecRec['specimen_volume']=""
if units=="1" or "":
ErSpecRec['specimen_weight']='%10.3e'%(vol*1e-3)
else:
ErSpecRec['specimen_weight']='%10.3e'%(vol)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
ErSampRec['sample_height']=info[-6]
else:
ErSampRec['sample_height']='0'
ErSampRec['sample_azimuth']='%7.1f'%(sample_azimuth)
ErSampRec['sample_dip']='%7.1f'%(sample_dip)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dip_direction)
ErSampRec['sample_class']=''
ErSampRec['sample_type']=''
ErSampRec['sample_lithology']=''
if Cdec!=0 or Cdec!="":
ErSampRec['magic_method_codes']='SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
if line == '\n': continue
MeasRec=ErSpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type=line[0:3]
if treat_type[1] == '.':
treat_type = 'NRM'
treat=line[2:6]
try: float(treat)
except ValueError: treat = line[3:6]
if treat_type.startswith('NRM'):
MeasRec['magic_method_codes']='LT-NO'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif treat_type.startswith('AF'):
MeasRec['magic_method_codes']='LT-AF-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('ARM'):
MeasRec['magic_method_codes']="LP-ARM"
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['magic_method_codes']="LP-ARM-AFD"
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('TT'):
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['measurement_temp']='273'
if treat.strip() == '':
MeasRec['treatment_temp']='273'
else:
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif treat_type.startswith('LT') or treat_type.startswith('LN2'):
MeasRec['magic_method_codes']='LT-LT-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='77'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif line[4] == '0': #assume decimal IZZI format 0 field thus can hardcode the dc fields
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']=str(int(treat_type) + 273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif line[4] == '1': #assume decimal IZZI format in constant field
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['magic_method_codes']='LT-T-I'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']=str(int(treat_type) + 273)
MeasRec['treatment_dc_field']='%1.2e'%DC_FIELD
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
elif line[4] == '2': #assume decimal IZZI format PTRM step
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['magic_method_codes']='LT-PTRM-I'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']=str(int(treat_type) + 273)
MeasRec['treatment_dc_field']='%1.2e'%DC_FIELD
MeasRec['treatment_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treatment_ac_field']='0'
else:
print("trouble with your treatment steps")
MeasRec['measurement_dec']=line[46:51]
MeasRec['measurement_inc']=line[52:58]
M='%8.2e'%(float(line[31:39])*vol*1e-3) # convert to Am2
MeasRec['measurement_magn_moment']=M
MeasRec['measurement_csd']='%7.1f'%(eval(line[41:46]))
MeasRec["measurement_positions"]='1'
MeasRec['measurement_standard']='u'
if len(line)>60:
MeasRec['magic_instrument_codes']=line[85:]
MeasRec['measurement_sd_x']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['measurement_sd_z']='%8.2e'%(float(line[76:85])*1e-8)
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site=pmag.parse_site(sample,samp_con,Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
pmag.magic_write(spec_file,ErSpecs,'er_specimens')
print('specimens stored in ',spec_file)
pmag.magic_write(samp_file,ErSamps,'er_samples')
print('samples stored in ',samp_file)
pmag.magic_write(site_file,ErSites,'er_sites')
print('sites stored in ', site_file)
Fixed=pmag.measurements_methods(MeasRecs,avg)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print('data stored in ',meas_file)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
iodp_srm_magic.py
DESCRIPTION
converts IODP LIMS and LORE SRM archive half sample format files to magic_measurements format files
SYNTAX
iodp_srm_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-A : don't average replicate measurements
INPUTS
IODP .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
csv_file=''
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
depth_method='a'
# get command line args
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
csv_file=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file = args[ind+1]
if '-Fsi' in args:
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file = args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
spec_file = kwargs.get('spec_file', 'er_specimens.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
# format variables
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
Specs,file_type = pmag.magic_read(spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSamps,file_type = pmag.magic_read(samp_file)
site_file = os.path.join(output_dir_path, site_file)
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist=[csv_file]
# parsing the data
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs,SiteRecs=[],[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
file_found = False
for f in filelist: # parse each file
if f[-3:].lower()=='csv':
file_found = True
print('processing: ',f)
full_file = os.path.join(input_dir_path, f)
with open(full_file, 'r') as fin:
file_input = fin.readlines()
keys=file_input[0].replace('\n','').split(',') # splits on underscores
if "Interval Top (cm) on SHLF" in keys:interval_key="Interval Top (cm) on SHLF"
if " Interval Bot (cm) on SECT" in keys:interval_key=" Interval Bot (cm) on SECT"
if "Offset (cm)" in keys: interval_key="Offset (cm)"
if "Top Depth (m)" in keys:depth_key="Top Depth (m)"
if "CSF-A Top (m)" in keys:depth_key="CSF-A Top (m)"
if "Depth CSF-A (m)" in keys:depth_key="Depth CSF-A (m)"
if "CSF-B Top (m)" in keys:
comp_depth_key="CSF-B Top (m)" # use this model if available
elif "Depth CSF-B (m)" in keys:
comp_depth_key="Depth CSF-B (m)"
else:
comp_depth_key=""
if "Demag level (mT)" in keys:demag_key="Demag level (mT)"
if "Demag Level (mT)" in keys: demag_key="Demag Level (mT)"
if "Inclination (Tray- and Bkgrd-Corrected) (deg)" in keys:inc_key="Inclination (Tray- and Bkgrd-Corrected) (deg)"
if "Inclination background + tray corrected (deg)" in keys:inc_key="Inclination background + tray corrected (deg)"
if "Inclination background + tray corrected (\xc2\xb0)" in keys:inc_key="Inclination background + tray corrected (\xc2\xb0)"
if "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
if "Declination (Tray- and Bkgrd-Corrected) (deg)" in keys:dec_key="Declination (Tray- and Bkgrd-Corrected) (deg)"
if "Declination background + tray corrected (deg)" in keys:dec_key="Declination background + tray corrected (deg)"
if "Declination background + tray corrected (\xc2\xb0)" in keys:dec_key="Declination background + tray corrected (\xc2\xb0)"
if "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
if "Intensity (Tray- and Bkgrd-Corrected) (A/m)" in keys:int_key="Intensity (Tray- and Bkgrd-Corrected) (A/m)"
if "Intensity background + tray corrected (A/m)" in keys:int_key="Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
if "Core Type" in keys:
core_type="Core Type"
else: core_type="Type"
if 'Run Number' in keys: run_number_key='Run Number'
if 'Test No.' in keys: run_number_key='Test No.'
if 'Test Changed On' in keys: date_key='Test Changed On'
if "Timestamp (UTC)" in keys: date_key="Timestamp (UTC)"
if "Section" in keys: sect_key="Section"
if "Sect" in keys: sect_key="Sect"
if 'Section Half' in keys: half_key='Section Half'
if "A/W" in keys: half_key="A/W"
if "Text ID" in keys: text_id="Text ID"
if "Text Id" in keys: text_id="Text Id"
for line in file_input[1:]:
InRec={}
test=0
recs=line.split(',')
for k in range(len(keys)):
if len(recs)==len(keys):
InRec[keys[k]]=line.split(',')[k]
if InRec['Exp']!="": test=1 # get rid of pesky blank lines
if test==1:
run_number=""
inst="IODP-SRM"
volume='15.59' # set default volume to this
MagRec,SpecRec,SampRec,SiteRec={},{},{},{}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
# Maintain backward compatibility for the ever-changing LIMS format (Argh!)
while len(InRec['Core'])<3:
InRec['Core']='0'+InRec['Core']
if "Last Tray Measurment" in list(InRec.keys()) and "SHLF" not in InRec[text_id] or 'dscr' in csv_file : # assume discrete sample
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"-"+InRec[sect_key]+'-'+InRec[half_key]+'-'+str(InRec[interval_key])
else: # mark as continuous measurements
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"_"+InRec[sect_key]+InRec[half_key]+'-'+str(InRec[interval_key])
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_citation_names']=citation
for key in list(SpecRec.keys()):SampRec[key]=SpecRec[key]
for key in list(SpecRec.keys()):SiteRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['sample_core_depth']=InRec[depth_key]
if comp_depth_key!='':
SampRec['sample_composite_depth']=InRec[comp_depth_key]
if "SHLF" not in InRec[text_id]:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
else:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SO-V'
SpecRec['er_specimen_name']=specimen
SpecRec['er_sample_name']=specimen
SampRec['er_sample_name']=specimen
SampRec['er_specimen_names']=specimen
SiteRec['er_specimen_names']=specimen
for key in list(SpecRec.keys()):MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
#MagRec['er_analyst_mail_names']=InRec['Test Entered By']
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
SpecRec['er_specimen_alternatives']=InRec[text_id]
if 'Sample Area (cm?)' in list(InRec.keys()) and InRec['Sample Area (cm?)']!= "": volume=InRec['Sample Area (cm?)']
if InRec[run_number_key]!= "": run_number=InRec[run_number_key]
datestamp=InRec[date_key].split() # date time is second line of file
if '/' in datestamp[0]:
mmddyy=datestamp[0].split('/') # break into month day year
if len(mmddyy[0])==1: mmddyy[0]='0'+mmddyy[0] # make 2 characters
if len(mmddyy[1])==1: mmddyy[1]='0'+mmddyy[1] # make 2 characters
if len(datestamp[1])==1: datestamp[1]='0'+datestamp[1] # make 2 characters
date='20'+mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]+":00.00"
if '-' in datestamp[0]:
mmddyy=datestamp[0].split('-') # break into month day year
date=mmddyy[0]+':'+mmddyy[1]+":"+mmddyy[2] +':' +datestamp[1]+":00.00"
MagRec["measurement_date"]=date
MagRec["magic_method_codes"]='LT-NO'
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
if 'Treatment Type' in list(InRec.keys()) and InRec['Treatment Type']!="":
if 'Alternating Frequency' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':I`ODP-DTECH' # measured on shipboard Dtech D2000
treatment_value=float(InRec['Treatment Value'])*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif 'Thermal' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec['Treatment Value'])+273 # convert C => K
MagRec["treatment_temp"]='%8.3e'%(treatment_value) #
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_number!="":
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
MagRec['measurement_inc']=InRec[inc_key].strip('"')
MagRec['measurement_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_csd']=''
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if MagRec['er_site_name'] not in sites:
sites.append(MagRec['er_site_name'])
SiteRecs.append(SiteRec)
#except:
# print 'Boo-boo somewhere - no idea where'
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
if len(SpecRecs)>0:
print('spec_file', spec_file)
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
#print 'specimens stored in ',spec_file
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
#print 'samples stored in ',samp_file
if len(SiteRecs)>0:
pmag.magic_write(site_file,SiteRecs,'er_sites')
#print 'sites stored in ',site_file
MagSort=pmag.sortbykeys(MagRecs,["er_specimen_name","treatment_ac_field"])
MagOuts=[]
for MagRec in MagSort:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec['treatment_ac_field']) # convert to string
MagOuts.append(MagRec)
Fixed=pmag.measurements_methods(MagOuts,noave)
if pmag.magic_write(meas_file,Fixed,'magic_measurements'):
print('data stored in ',meas_file)
return True, meas_file
else:
print('no data found. bad magfile?')
return False, 'no data found. bad magfile?'
def main():
"""
NAME
mini_magic.py
DESCRIPTION
converts the Yale minispin format to magic_measurements format files
SYNTAX
mini_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, required
-F FILE: specify output file, default is magic_measurements.txt
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
-vol: volume assumed for measurement in cm^3
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
[10] LL-SI-SA-SP_STEP where LL is location, SI is site, SA is sample and SP is specimen and STEP is demagnetization step
INPUT
Must put separate experiments (all AF, thermal, etc.) in
seperate files
Format of Yale MINI files:
LL-SI-SP_STEP, Declination, Inclination, Intensity (mA/m), X,Y,Z
"""
# initialize some stuff
noave = 0
methcode, inst = "LP-NO", ""
samp_con, Z = '10', 1
demag = "N"
er_location_name = ""
citation = 'This study'
args = sys.argv
coil = ""
volume = 10e-6 # assume a volume of 10cc
#
# get command line arguments
#
user = ""
dir_path = './'
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = dir_path + args[ind + 1]
else:
meas_file = dir_path + 'magic_measurements.txt'
if '-f' in args:
ind = args.index("-f")
magfile = dir_path + args[ind + 1]
try:
input = open(magfile, 'r')
except:
print("bad mag file name")
sys.exit()
else:
print("mag_file field is required option")
print(main.__doc__)
sys.exit()
specnum = 0
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 "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-vol" in args:
ind = args.index("-vol")
volume = 1e-6 * float(args[ind + 1])
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'
methcode = "LT-AF-Z"
if "T" in codes:
demag = "T"
MagRecs = []
version_num = pmag.get_version()
for line in input.readlines():
rec = line.split(',')
if len(rec) > 1:
MagRec = {}
IDs = rec[0].split('_')
treat = IDs[1]
MagRec["er_specimen_name"] = IDs[0]
print(MagRec['er_specimen_name'])
sids = IDs[0].split('-')
MagRec['er_location_name'] = sids[0]
MagRec['er_site_name'] = sids[0] + '-' + sids[1]
if len(sids) == 2:
MagRec["er_sample_name"] = IDs[0]
else:
MagRec[
"er_sample_name"] = sids[0] + '-' + sids[1] + '-' + sids[2]
print(MagRec)
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"
if demag == "AF":
MagRec["treatment_ac_field"] = '%8.3e' % (
float(treat) * 1e-3) # peak field in tesla
if demag == "T":
meas_type = "LT-T-Z"
MagRec["treatment_dc_field"] = '%8.3e' % (0)
MagRec["treatment_temp"] = '%8.3e' % (float(treat) + 273.
) # temp in kelvin
if demag == "N":
meas_type = "LT-NO"
MagRec["treatment_ac_field"] = '0'
MagRec["treatment_dc_field"] = '0'
MagRec["measurement_magn_moment"] = '%10.3e' % (
volume * float(rec[3]) * 1e-3) # moment in Am2 (from mA/m)
MagRec["measurement_dec"] = rec[1]
MagRec["measurement_inc"] = rec[2]
MagRec["magic_instrument_codes"] = inst
MagRec["er_analyst_mail_names"] = user
MagRec["er_citation_names"] = citation
MagRec["magic_method_codes"] = methcode.strip(':')
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
def main(command_line=True, **kwargs):
"""
NAME
iodp_srm_magic.py
DESCRIPTION
converts IODP LIMS and LORE SRM archive half sample format files to magic_measurements format files
SYNTAX
iodp_srm_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-A : don't average replicate measurements
INPUTS
IODP .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
csv_file=''
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
depth_method='a'
# get command line args
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
csv_file=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file = args[ind+1]
if '-Fsi' in args:
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file = args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
spec_file = kwargs.get('spec_file', 'er_specimens.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
# format variables
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
Specs,file_type = pmag.magic_read(spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSamps,file_type = pmag.magic_read(samp_file)
site_file = os.path.join(output_dir_path, site_file)
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist=[csv_file]
# parsing the data
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs,SiteRecs=[],[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
file_found = False
for f in filelist: # parse each file
if f[-3:].lower()=='csv':
file_found = True
print 'processing: ',f
full_file = os.path.join(input_dir_path, f)
file_input=open(full_file,'rU').readlines()
keys=file_input[0].replace('\n','').split(',') # splits on underscores
if "Interval Top (cm) on SHLF" in keys:interval_key="Interval Top (cm) on SHLF"
if " Interval Bot (cm) on SECT" in keys:interval_key=" Interval Bot (cm) on SECT"
if "Offset (cm)" in keys: interval_key="Offset (cm)"
if "Top Depth (m)" in keys:depth_key="Top Depth (m)"
if "CSF-A Top (m)" in keys:depth_key="CSF-A Top (m)"
if "Depth CSF-A (m)" in keys:depth_key="Depth CSF-A (m)"
if "CSF-B Top (m)" in keys:
comp_depth_key="CSF-B Top (m)" # use this model if available
elif "Depth CSF-B (m)" in keys:
comp_depth_key="Depth CSF-B (m)"
else:
comp_depth_key=""
if "Demag level (mT)" in keys:demag_key="Demag level (mT)"
if "Demag Level (mT)" in keys: demag_key="Demag Level (mT)"
if "Inclination (Tray- and Bkgrd-Corrected) (deg)" in keys:inc_key="Inclination (Tray- and Bkgrd-Corrected) (deg)"
if "Inclination background + tray corrected (deg)" in keys:inc_key="Inclination background + tray corrected (deg)"
if "Inclination background + tray corrected (\xc2\xb0)" in keys:inc_key="Inclination background + tray corrected (\xc2\xb0)"
if "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
if "Declination (Tray- and Bkgrd-Corrected) (deg)" in keys:dec_key="Declination (Tray- and Bkgrd-Corrected) (deg)"
if "Declination background + tray corrected (deg)" in keys:dec_key="Declination background + tray corrected (deg)"
if "Declination background + tray corrected (\xc2\xb0)" in keys:dec_key="Declination background + tray corrected (\xc2\xb0)"
if "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
if "Intensity (Tray- and Bkgrd-Corrected) (A/m)" in keys:int_key="Intensity (Tray- and Bkgrd-Corrected) (A/m)"
if "Intensity background + tray corrected (A/m)" in keys:int_key="Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
if "Core Type" in keys:
core_type="Core Type"
else: core_type="Type"
if 'Run Number' in keys: run_number_key='Run Number'
if 'Test No.' in keys: run_number_key='Test No.'
if 'Test Changed On' in keys: date_key='Test Changed On'
if "Timestamp (UTC)" in keys: date_key="Timestamp (UTC)"
if "Section" in keys: sect_key="Section"
if "Sect" in keys: sect_key="Sect"
if 'Section Half' in keys: half_key='Section Half'
if "A/W" in keys: half_key="A/W"
if "Text ID" in keys: text_id="Text ID"
if "Text Id" in keys: text_id="Text Id"
for line in file_input[1:]:
InRec={}
test=0
recs=line.split(',')
for k in range(len(keys)):
if len(recs)==len(keys):
InRec[keys[k]]=line.split(',')[k]
if InRec['Exp']!="": test=1 # get rid of pesky blank lines
if test==1:
run_number=""
inst="IODP-SRM"
volume='15.59' # set default volume to this
MagRec,SpecRec,SampRec,SiteRec={},{},{},{}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
# Maintain backward compatibility for the ever-changing LIMS format (Argh!)
while len(InRec['Core'])<3:
InRec['Core']='0'+InRec['Core']
if "Last Tray Measurment" in InRec.keys() and "SHLF" not in InRec[text_id] or 'dscr' in csv_file : # assume discrete sample
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"-"+InRec[sect_key]+'-'+InRec[half_key]+'-'+str(InRec[interval_key])
else: # mark as continuous measurements
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"_"+InRec[sect_key]+InRec[half_key]+'-'+str(InRec[interval_key])
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_citation_names']=citation
for key in SpecRec.keys():SampRec[key]=SpecRec[key]
for key in SpecRec.keys():SiteRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['sample_core_depth']=InRec[depth_key]
if comp_depth_key!='':
SampRec['sample_composite_depth']=InRec[comp_depth_key]
if "SHLF" not in InRec[text_id]:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
else:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SO-V'
SpecRec['er_specimen_name']=specimen
SpecRec['er_sample_name']=specimen
SampRec['er_sample_name']=specimen
SampRec['er_specimen_names']=specimen
SiteRec['er_specimen_names']=specimen
for key in SpecRec.keys():MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
#MagRec['er_analyst_mail_names']=InRec['Test Entered By']
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
SpecRec['er_specimen_alternatives']=InRec[text_id]
if 'Sample Area (cm?)' in InRec.keys() and InRec['Sample Area (cm?)']!= "": volume=InRec['Sample Area (cm?)']
if InRec[run_number_key]!= "": run_number=InRec[run_number_key]
datestamp=InRec[date_key].split() # date time is second line of file
if '/' in datestamp[0]:
mmddyy=datestamp[0].split('/') # break into month day year
if len(mmddyy[0])==1: mmddyy[0]='0'+mmddyy[0] # make 2 characters
if len(mmddyy[1])==1: mmddyy[1]='0'+mmddyy[1] # make 2 characters
if len(datestamp[1])==1: datestamp[1]='0'+datestamp[1] # make 2 characters
date='20'+mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]+":00.00"
if '-' in datestamp[0]:
mmddyy=datestamp[0].split('-') # break into month day year
date=mmddyy[0]+':'+mmddyy[1]+":"+mmddyy[2] +':' +datestamp[1]+":00.00"
MagRec["measurement_date"]=date
MagRec["magic_method_codes"]='LT-NO'
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
if 'Treatment Type' in InRec.keys() and InRec['Treatment Type']!="":
if 'Alternating Frequency' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':I`ODP-DTECH' # measured on shipboard Dtech D2000
treatment_value=float(InRec['Treatment Value'])*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif 'Thermal' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec['Treatment Value'])+273 # convert C => K
MagRec["treatment_temp"]='%8.3e'%(treatment_value) #
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_number!="":
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
MagRec['measurement_inc']=InRec[inc_key].strip('"')
MagRec['measurement_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_csd']=''
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if MagRec['er_site_name'] not in sites:
sites.append(MagRec['er_site_name'])
SiteRecs.append(SiteRec)
#except:
# print 'Boo-boo somewhere - no idea where'
if not file_found:
print "No .csv files were found"
return False, "No .csv files were found"
if len(SpecRecs)>0:
print 'spec_file', spec_file
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
#print 'specimens stored in ',spec_file
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
#print 'samples stored in ',samp_file
if len(SiteRecs)>0:
pmag.magic_write(site_file,SiteRecs,'er_sites')
#print 'sites stored in ',site_file
MagSort=pmag.sortbykeys(MagRecs,["er_specimen_name","treatment_ac_field"])
MagOuts=[]
for MagRec in MagSort:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec['treatment_ac_field']) # convert to string
MagOuts.append(MagRec)
Fixed=pmag.measurements_methods(MagOuts,noave)
if pmag.magic_write(meas_file,Fixed,'magic_measurements'):
print 'data stored in ',meas_file
return True, meas_file
else:
print 'no data found. bad magfile?'
return False, 'no data found. bad magfile?'
def main(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-WD Working Directory: output directory where files are going to go
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-dc B PHI THETA: dc lab field (in microTesla), phi,and theta must be input as a tuple "(DC,PHI,THETA)". If not input user will be asked for values, this is advantagious if there are differing dc fields between steps or specimens. Note: this currently only works with the decimal IZZI naming convetion (XXX.0,1,2 where XXX is the treatment temperature and 0 is a zero field step, 1 is in field, and 2 is a pTRM check). All other steps are hardcoded dc_field = 0.
INPUT
Best to put separate experiments in separate files (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
NOTES:
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: default] 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 = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] or [email protected] for help.
"""
#
# 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
#
#initialize variables
norm = 'cc'
samp_con, Z = '3', 1
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
ErSpecs, ErSamps, ErSites, ErLocs, ErCits = [], [], [], [], []
MeasRecs = []
specnum, units, locname = 0, "1", "unknown"
citation = "This study"
dir_path = '.'
args = sys.argv
if command_line:
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
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 '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
if '-Fsi' in args: # LORI addition
ind = args.index("-Fsi")
site_file = args[ind + 1]
if '-loc' in args:
ind = args.index("-loc")
locname = args[ind + 1]
if '-mcd' in args:
ind = args.index("-mcd")
methods = args[ind + 1]
else:
methods = 'SO-MAG'
if '-spc' in args:
ind = args.index("-spc")
specnum = -int(args[ind + 1])
if '-n' in args:
ind = args.index("-n")
norm = args[ind + 1]
if "-A" in args:
avg = 1
else:
avg = 0
if '-dc' in args:
ind = args.index('-dc')
DC_FIELD, DC_PHI, DC_THETA = list(
map(float, args[ind + 1].strip('( ) [ ]').split(',')))
DC_FIELD *= 1e-6
yn = ''
GET_DC_PARAMS = False
else:
GET_DC_PARAMS, DC_FIELD, DC_PHI, DC_THETA, yn = True, 0, 0, -90, ''
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")
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 "7" in samp_con:
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"
if '-f' in args:
ind = args.index("-f")
magfile = args[ind + 1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind + 1]
else:
input_dir_path = os.path.split(magfile)[0]
output_dir_path = dir_path
# LJ
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file',
'magic_measurements.txt') # outfile
spec_file = kwargs.get('spec_file',
'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path',
os.path.split(magfile)[0])
output_dir_path = dir_path
DC_FIELD, DC_PHI, DC_THETA = list(
map(float, kwargs.get('dc_params', (0, 0, -90))))
DC_FIELD *= 1e-6
yn = ''
if DC_FIELD == 0 and DC_PHI == 0 and DC_THETA == -90:
GET_DC_PARAMS = True
else:
GET_DC_PARAMS = False
# done with module-specific stuff
# formatting and checking variables
if "4" in samp_con:
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 "7" in samp_con:
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"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file = os.path.join(output_dir_path, meas_file)
FIRST_GET_DC = True
try:
with open(magfile, 'r') as file_input:
File = file_input.readlines()
except Exception as ex:
print("bad sam file name: ", magfile)
return False, "bad sam file name"
if len(File) == 1:
File = File[0].split('\r')
File = [x + "\r\n" for x in File]
sids, ln, format = [], 0, 'CIT'
formats = ['CIT', '2G', 'APP', 'JRA']
if File[ln].strip() == 'CIT': ln += 1
ErLocRec = {}
ErLocRec["er_location_name"] = locname
ErLocRec["er_citation_names"] = citation
comment = File[ln]
if comment == 'CIT':
format = comment
ln += 1
comment = File[ln]
print(comment)
ln += 1
specimens, samples, sites = [], [], []
if format == 'CIT':
line = File[ln].split()
site_lat = line[0]
site_lon = line[1]
ErLocRec["location_begin_lat"] = site_lat
ErLocRec["location_begin_lon"] = site_lon
ErLocRec["location_end_lat"] = site_lat
ErLocRec["location_end_lon"] = site_lon
ErLocs.append(ErLocRec)
try:
Cdec = float(line[2])
except ValueError:
pdb.set_trace()
for k in range(ln + 1, len(File)):
line = File[k]
rec = line.split()
if rec == []: continue
specimen = rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec, ErSampRec, ErSiteRec = {}, {}, {}
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
ErSpecRec['er_specimen_name'] = specimen
ErSpecRec['er_sample_name'] = sample
ErSpecRec['er_site_name'] = site
ErSpecRec['er_location_name'] = locname
ErSpecRec['er_citation_names'] = citation
ErSampRec['er_sample_name'] = sample
ErSampRec['er_site_name'] = site
ErSampRec['er_location_name'] = locname
ErSampRec['er_citation_names'] = citation
ErSampRec['magic_method_codes'] = methods
ErSampRec['sample_declination_correction'] = '%7.1f' % (Cdec)
ErSiteRec['er_site_name'] = site
ErSiteRec['er_location_name'] = locname
ErSiteRec['er_citation_names'] = citation
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
with open(os.path.join(input_dir_path, specimen), 'r') as finput:
Lines = list(finput.readlines())
comment = ""
line = Lines[0].split()
if len(line) > 2:
comment = line[2]
info = Lines[1].split()
vol = float(info[-1])
if vol != 1.0:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSpecRec['specimen_weight'] = ""
if units == "1" or "":
ErSpecRec['specimen_volume'] = '%10.3e' % (vol * 1e-6)
else:
ErSpecRec['specimen_volume'] = '%10.3e' % (vol)
else:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSpecRec['specimen_volume'] = ""
if units == "1" or "":
ErSpecRec['specimen_weight'] = '%10.3e' % (vol * 1e-3)
else:
ErSpecRec['specimen_weight'] = '%10.3e' % (vol)
dip = float(info[-2])
dip_direction = float(info[-3]) + Cdec + 90.
sample_dip = -float(info[-4])
sample_azimuth = float(info[-5]) + Cdec - 90.
if len(info) > 5:
ErSampRec['sample_height'] = info[-6]
else:
ErSampRec['sample_height'] = '0'
ErSampRec['sample_azimuth'] = '%7.1f' % (sample_azimuth)
ErSampRec['sample_dip'] = '%7.1f' % (sample_dip)
ErSampRec['sample_bed_dip'] = '%7.1f' % (dip)
ErSampRec['sample_bed_dip_direction'] = '%7.1f' % (dip_direction)
ErSampRec['sample_class'] = ''
ErSampRec['sample_type'] = ''
ErSampRec['sample_lithology'] = ''
if Cdec != 0 or Cdec != "":
ErSampRec['magic_method_codes'] = 'SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes'] = 'SO-MAG'
for line in Lines[2:len(Lines)]:
if line == '\n': continue
MeasRec = ErSpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type = line[0:3]
if treat_type[1] == '.':
treat_type = 'NRM'
treat = line[2:6]
try:
float(treat)
except ValueError:
treat = line[3:6]
if treat_type.startswith('NRM'):
MeasRec['magic_method_codes'] = 'LT-NO'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif treat_type.startswith('AF'):
MeasRec['magic_method_codes'] = 'LT-AF-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
if treat.strip() == '':
MeasRec['treatment_ac_field'] = '0'
else:
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.startswith('ARM'):
MeasRec['magic_method_codes'] = "LP-ARM"
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
if treat.strip() == '':
MeasRec['treatment_ac_field'] = '0'
else:
MeasRec['magic_method_codes'] = "LP-ARM-AFD"
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.startswith('TT'):
MeasRec['magic_method_codes'] = 'LT-T-Z'
MeasRec['measurement_temp'] = '273'
if treat.strip() == '':
MeasRec['treatment_temp'] = '273'
else:
MeasRec['treatment_temp'] = '%7.1f' % (float(treat) + 273)
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif treat_type.startswith('LT') or treat_type.startswith('LN2'):
MeasRec['magic_method_codes'] = 'LT-LT-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '77'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif line[
4] == '0': #assume decimal IZZI format 0 field thus can hardcode the dc fields
MeasRec['magic_method_codes'] = 'LT-T-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = str(int(treat_type) + 273)
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif line[4] == '1': #assume decimal IZZI format in constant field
if GET_DC_PARAMS:
GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(
FIRST_GET_DC, specimen, treat_type, yn)
MeasRec['magic_method_codes'] = 'LT-T-I'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = str(int(treat_type) + 273)
MeasRec['treatment_dc_field'] = '%1.2e' % DC_FIELD
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
elif line[4] == '2': #assume decimal IZZI format PTRM step
if GET_DC_PARAMS:
GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(
FIRST_GET_DC, specimen, treat_type, yn)
MeasRec['magic_method_codes'] = 'LT-PTRM-I'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = str(int(treat_type) + 273)
MeasRec['treatment_dc_field'] = '%1.2e' % DC_FIELD
MeasRec['treatment_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treatment_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['treatment_ac_field'] = '0'
else:
print("trouble with your treatment steps")
MeasRec['measurement_dec'] = line[46:51]
MeasRec['measurement_inc'] = line[52:58]
M = '%8.2e' % (float(line[31:39]) * vol * 1e-3) # convert to Am2
MeasRec['measurement_magn_moment'] = M
MeasRec['measurement_csd'] = '%7.1f' % (eval(line[41:46]))
MeasRec["measurement_positions"] = '1'
MeasRec['measurement_standard'] = 'u'
if len(line) > 60:
MeasRec['magic_instrument_codes'] = line[85:]
MeasRec['measurement_sd_x'] = '%8.2e' % (
float(line[58:67]) * 1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y'] = '%8.2e' % (float(line[67:76]) *
1e-8)
MeasRec['measurement_sd_z'] = '%8.2e' % (float(line[76:85]) *
1e-8)
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site = pmag.parse_site(sample, samp_con, Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
pmag.magic_write(spec_file, ErSpecs, 'er_specimens')
print('specimens stored in ', spec_file)
pmag.magic_write(samp_file, ErSamps, 'er_samples')
print('samples stored in ', samp_file)
pmag.magic_write(site_file, ErSites, 'er_sites')
print('sites stored in ', site_file)
Fixed = pmag.measurements_methods(MeasRecs, avg)
pmag.magic_write(meas_file, Fixed, 'magic_measurements')
print('data stored in ', meas_file)
return True, meas_file
def main():
"""
NAME
odp_srm_magic.py
DESCRIPTION
converts ODP measurement format files to magic_measurements format files
SYNTAX
odp_srm_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsa FILE: specify output er_sample.txt file, default is er_sample.txt
-A : don't average replicate measurements
INPUT
put data from a single core into a directory. depths will be below core top
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
samp_file='er_samples.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0,
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-A" in args: noave=1
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]
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=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 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
samp_file=dir_path+'/'+samp_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for file in filelist: # parse each file
if file[-3:].lower()=='srm':
print('processing: ',file)
Nfo=file.split('_')[0].split('-')
try:
sect=int(Nfo[3][:-1])
except:
sect=1
input=open(file,'r').readlines()
MagRec,SpecRec,SampRec={},{},{}
alt_spec,treatment_type,treatment_value,user="","","",""
inst="ODP-SRM"
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_code']='FS-C-DRILL-IODP:SP-SS-C'
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
treatment_value,inst="","ODP-SRM"
k=0
while 1:
fields= input[k].replace('\n','').split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
if "treatment_value" in fields[0]:
value=fields[1]
if value!=" ":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]='%8.3e'%(treatment_value) # AF demag in treat mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
k+=1
if input[k][0:7]=='<MULTI>':
break
while 1:
k+=1
line = input[k]
if line[0:5]=='<RAW>':
break
treatment_value=""
rec=line.replace('\n','').split(',') # list of data
if len(rec)>2:
MeasRec,SampRec={},{'core_depth':'0','er_sample_name':'0','er_site_name':'0','er_location_name':'location'}
for key in list(MagRec.keys()):MeasRec[key]=MagRec[key]
for item in rec:
items=item.split('=')
if 'demag_level' in items[0]:
treat= float(items[1])
if treat!=0:
MeasRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MeasRec["treatment_ac_field"]='%8.3e'%(treat*1e-3) # AF demag in treat mT => T
if 'inclination_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_inc']=items[1]
if 'declination_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_dec']=items[1]
if 'intensity_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
MeasRec['magic_instrument_codes']=inst
if 'offset' in items[0]:
depth='%7.3f'%(float(sect-1)*1.5+float(items[1]))
SampRec['core_depth']=depth
MeasRec['er_specimen_name']=depth
MeasRec['er_sample_name']=depth
MeasRec['er_site_name']=depth
MeasRec['er_location_name']='location'
SampRec['er_sample_name']=depth
SampRec['er_site_name']=depth
SampRec['er_location_name']='location'
MeasRec['measurement_number']='1'
SampRecs.append(SampRec)
MagRecs.append(MeasRec)
pmag.magic_write(samp_file,SampRecs,'er_samples')
print('samples stored in ',samp_file)
Fixed=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print('data stored in ',meas_file)
def cit_magic(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-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
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
NOTES:
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 = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
"""
#
#initialize variables
norm = 'cc'
samp_con, Z = '3', 1
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
ErSpecs, ErSamps, ErSites, ErLocs, ErCits = [], [], [], [], []
MeasRecs = []
specnum, units, locname = 0, "1", "unknown"
citation = "This study"
dir_path = '.'
args = sys.argv
if command_line:
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
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 '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
if '-Fsi' in args: # LORI addition
ind = args.index("-Fsi")
site_file = args[ind + 1]
if '-loc' in args:
ind = args.index("-loc")
locname = args[ind + 1]
if '-mcd' in args:
ind = args.index("-mcd")
methods = args[ind + 1]
else:
methods = 'SO-MAG'
if '-spc' in args:
ind = args.index("-spc")
specnum = -int(args[ind + 1])
if '-n' in args:
ind = args.index("-n")
norm = args[ind + 1]
if "-A" in args:
avg = 1
else:
avg = 0
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"
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 '-f' in args:
ind = args.index("-f")
magfile = args[ind + 1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
# LJ
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file',
'magic_measurements.txt') # outfile
spec_file = kwargs.get('spec_file',
'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
# done with module-specific stuff
# formatting and checking variables
if "4" in samp_con:
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"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file = os.path.join(output_dir_path, meas_file)
try:
file_input = open(magfile, 'r')
except Exception as ex:
print "bad sam file name: ", magfile
return False, "bad sam file name"
File = file_input.readlines()
if len(File) == 1:
File = File[0].split('\r')
File = map(lambda x: x + "\r\n", File)
sids, ln, format = [], 0, 'CIT'
formats = ['CIT', '2G', 'APP', 'JRA']
if File[ln].strip() == 'CIT': ln += 1
ErLocRec = {}
ErLocRec["er_location_name"] = locname
ErLocRec["er_citation_names"] = citation
comment = File[ln]
if comment == 'CIT':
format = comment
ln += 1
comment = File[ln]
#print comment
ln += 1
specimens, samples, sites = [], [], []
if format == 'CIT':
line = File[ln].split()
site_lat = line[0]
site_lon = line[1]
ErLocRec["location_begin_lat"] = site_lat
ErLocRec["location_begin_lon"] = site_lon
ErLocRec["location_end_lat"] = site_lat
ErLocRec["location_end_lon"] = site_lon
ErLocs.append(ErLocRec)
try:
Cdec = float(line[2])
except ValueError:
pdb.set_trace()
for k in range(ln + 1, len(File)):
line = File[k]
rec = line.split()
if rec == []: continue
specimen = rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec, ErSampRec, ErSiteRec = {}, {}, {}
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
ErSpecRec['er_specimen_name'] = specimen
ErSpecRec['er_sample_name'] = sample
ErSpecRec['er_site_name'] = site
ErSpecRec['er_location_name'] = locname
ErSpecRec['er_citation_names'] = citation
ErSampRec['er_sample_name'] = sample
ErSampRec['er_site_name'] = site
ErSampRec['er_location_name'] = locname
ErSampRec['er_citation_names'] = citation
ErSampRec['magic_method_codes'] = methods
ErSampRec['sample_declination_correction'] = '%7.1f' % (Cdec)
ErSiteRec['er_site_name'] = site
ErSiteRec['er_location_name'] = locname
ErSiteRec['er_citation_names'] = citation
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
f = open(input_dir_path + '/' + specimen, 'rU')
Lines = f.readlines()
comment = ""
line = Lines[0].split()
if len(line) > 2:
comment = line[2]
info = Lines[1].split()
vol = float(info[-1])
if vol != 1.0:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSpecRec['specimen_weight'] = ""
if units == "1" or "":
ErSpecRec['specimen_volume'] = '%10.3e' % (vol * 1e-6)
else:
ErSpecRec['specimen_volume'] = '%10.3e' % (vol)
else:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSpecRec['specimen_volume'] = ""
if units == "1" or "":
ErSpecRec['specimen_weight'] = '%10.3e' % (vol * 1e-3)
else:
ErSpecRec['specimen_weight'] = '%10.3e' % (vol)
dip = float(info[-2])
dip_direction = float(info[-3]) + Cdec + 90.
sample_dip = -float(info[-4])
sample_azimuth = float(info[-5]) + Cdec - 90.
if len(info) > 5:
ErSampRec['sample_height'] = info[-6]
else:
ErSampRec['sample_height'] = '0'
ErSampRec['sample_azimuth'] = '%7.1f' % (sample_azimuth)
ErSampRec['sample_dip'] = '%7.1f' % (sample_dip)
ErSampRec['sample_bed_dip'] = '%7.1f' % (dip)
ErSampRec['sample_bed_dip_direction'] = '%7.1f' % (dip_direction)
ErSampRec['sample_class'] = ''
ErSampRec['sample_type'] = ''
ErSampRec['sample_lithology'] = ''
if Cdec != 0 or Cdec != "":
ErSampRec['magic_method_codes'] = 'SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes'] = 'SO-MAG'
for line in Lines[2:len(Lines)]:
#print 'line:', line
MeasRec = ErSpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type = line[0:3]
treat = line[2:6]
try:
float(treat)
except ValueError:
treat = line[3:6]
if treat_type.startswith('NRM'):
MeasRec['magic_method_codes'] = 'LT-NO'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
elif treat_type.startswith('AF'):
MeasRec['magic_method_codes'] = 'LT-AF-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
if treat.strip() == '':
MeasRec['treatment_ac_field'] = '0'
else:
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.startswith('ARM'):
MeasRec['magic_method_codes'] = "LP-ARM"
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
if treat.strip() == '':
MeasRec['treatment_ac_field'] = '0'
else:
MeasRec['magic_method_codes'] = "LP-ARM-AFD"
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.startswith('TT'):
MeasRec['magic_method_codes'] = 'LT-T-Z'
MeasRec['measurement_temp'] = '273'
if treat.strip() == '':
MeasRec['treatment_temp'] = '273'
else:
MeasRec['treatment_temp'] = '%7.1f' % (float(treat) + 273)
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
elif treat_type.startswith('LT') or treat_type.startswith('LN2'):
MeasRec['magic_method_codes'] = 'LT-LT-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '77'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
else:
print "trouble with your treatment steps"
MeasRec['measurement_dec'] = line[46:51]
MeasRec['measurement_inc'] = line[52:58]
M = '%8.2e' % (float(line[31:39]) * vol * 1e-3) # convert to Am2
MeasRec['measurement_magn_moment'] = M
MeasRec['measurement_csd'] = '%7.1f' % (eval(line[41:46]))
MeasRec["measurement_positions"] = '1'
MeasRec['measurement_standard'] = 'u'
if len(line) > 60:
MeasRec['magic_instrument_codes'] = line[85:]
MeasRec['measurement_sd_x'] = '%8.2e' % (
float(line[58:67]) * 1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y'] = '%8.2e' % (float(line[67:76]) *
1e-8)
MeasRec['measurement_sd_z'] = '%8.2e' % (float(line[76:85]) *
1e-8)
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site = pmag.parse_site(sample, samp_con, Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
er_specs = magic_write(spec_file, ErSpecs, 'er_specimens')
#print 'specimens stored in "er_specs"'
er_samps = magic_write(samp_file, ErSamps, 'er_samples')
#print 'samples stored in "er_samps"'
er_sites = magic_write(site_file, ErSites, 'er_sites')
#print 'sites stored in "er_sites"'
Fixed = pmag.measurements_methods(MeasRecs, avg)
magic_meas = magic_write(meas_file, Fixed, 'magic_measurements')
#print 'data stored in "magic_meas"'
return True, meas_file, str(er_specs), str(er_samps), str(er_sites), str(
magic_meas)
def main():
"""
NAME
odp_spn_magic.py
DESCRIPTION
converts ODP's Molspin's .spn format files to magic_measurements format files
SYNTAX
odp_spn_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify .spn format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-LP [AF, T, A FIELD, I N] specify one (FIELD is DC field in uT)
AF: af demag
T: thermal
A: anhysteretic remanence
I: isothermal remanence
N: NRM only
-v vol , specify volume used in MolSpin program in cm^3
-A: don't average replicate measurements
INPUT
Best to put separate experiments (all AF, thermal, ARM, etc. files in
seperate .spn files
Format of .spn files:
header with:
Leg Sit H Cor T Sec Top Bot Dec Inc Intens Demag. Stage
followed by data
Leg: Expedition number
Sit: is ODP Site
H: Hole letter
Cor: Core number
T: Core type (R,H,X,etc.)
Sec: section number
top: top of sample interval
bot: bottom of sample interval
Intens in mA/m
Demag Stage:
XXX T in Centigrade
XXX AF in mT
"""
# initialize some stuff
noave=0
methcode,inst="",""
phi,theta,peakfield,labfield=0,0,0,0
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]
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
trm=0
irm=0
dc="0"
dir_path='.'
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if "-WD" in args:
ind=args.index("-WD")
dir_path=args[ind+1]
samp_file=dir_path+'/'+'er_samples.txt'
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-f' in args:
ind=args.index("-f")
mag_file=dir_path+'/'+args[ind+1]
try:
input=open(mag_file,'r')
except:
print("bad mag file name")
sys.exit()
else:
print("spn_file field is required option")
print(main.__doc__)
sys.exit()
vol=10.5e-6 # default for spinner program
if "-V" in args:
ind=args.index("-V")
vol=float(args[ind+1])*1e-6 # convert volume to m^3
if "-A" in args: noave=1
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
methcode="LT-AF-Z"
if "T" in codes:
demag="T"
methcode="LT-T-Z"
if "I" in codes:
methcode="LP-IRM"
if "A" in codes:
methcode="LT-AF-I"
dc='%10.3e'%(1e-3*float(args[ind+1]))
MagRecs=[]
version_num=pmag.get_version()
meas_file=dir_path+'/'+meas_file
for line in input.readlines():
instcode="ODP-MSPN"
rec=line.split()
if len(rec)>2 and "Leg" not in line:
MagRec={}
MagRec['er_expedition_name']=rec[0]
MagRec['er_location_name']=rec[1]+rec[2]
MagRec["er_specimen_name"]=rec[0]+'-'+'U'+rec[1]+rec[2].upper()+"-"+rec[3]+rec[4].upper()+'-'+rec[5]+'-'+'W'+'-'+rec[6]
MagRec["er_site_name"]=MagRec['er_specimen_name']
MagRec["er_sample_name"]=MagRec['er_specimen_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"]=dc
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
if float(rec[11])==0:
pass
elif demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[11])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else:
MagRec["treatment_temp"]='%8.3e' % (float(rec[11])+273.) # temp in kelvin
meas_type="LT-T-Z"
intens=1e-3*float(rec[10])*vol # convert mA/m to Am^2
MagRec["measurement_magn_moment"]='%10.3e'% (intens)
MagRec["measurement_dec"]=rec[8]
MagRec["measurement_inc"]=rec[9]
MagRec["magic_instrument_codes"]="ODP-MSPN"
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["measurement_csd"]=''
MagRec["measurement_number"]='1'
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print("results put in ",meas_file)
def main(command_line=True, **kwargs):
"""
NAME
jr6_jr6_magic.py
DESCRIPTION
converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
jr6_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-JR IODP samples measured on the JOIDES RESOLUTION
-v NUM : specify the volume in cc of the sample, default 2.5^3cc
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.
INPUT
JR6 .jr6 format file
"""
# initialize some stuff
noave = 0
#volume=2.5**3 #default volume is a 2.5cm cube
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
inst = ""
samp_con, Z = '1', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
specnum = 1
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
user = ""
mag_file = ""
dir_path = '.'
MagRecs = []
ErSamps = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
tmp_file = "fixed.jr6"
meth_code, JR = "", 0
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
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]
#try:
# open(samp_file,'r')
# 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 = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args: noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
if "-JR" in args:
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
JR = 1
samp_con = '5'
if "-v" in args:
ind = args.index("-v")
volume = float(
args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
JR = kwargs.get('JR', 0)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
samp_con = '5'
# format variables
mag_file = input_dir_path + "/" + mag_file
meas_file = output_dir_path + "/" + meas_file
samp_file = output_dir_path + "/" + samp_file
tmp_file = output_dir_path + "/" + tmp_file
if specnum != 0:
specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
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")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
ErSampRec, ErSiteRec = {}, {}
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data = open(mag_file, 'r')
tmp_data = open(tmp_file, 'w')
line = pre_data.readline()
while line != '':
line = line.replace('-', ' -')
#print "line=", line
tmp_data.write(line)
line = pre_data.readline()
tmp_data.close()
pre_data.close()
data = pd.read_csv(tmp_file, delim_whitespace=True, header=None)
if JR == 0: #
data.columns = [
'er_specimen_name', 'step', 'x', 'y', 'z', 'expon',
'sample_azimuth', 'sample_dip', 'sample_bed_dip_direction',
'sample_bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2',
'param3', 'param4', 'measurement_csd'
]
cart = np.array([data['x'], data['y'], data['z']]).transpose()
else: # measured on the Joides Resolution JR6
data.columns = [
'er_specimen_name', 'step', 'negz', 'y', 'x', 'expon',
'sample_azimuth', 'sample_dip', 'sample_bed_dip_direction',
'sample_bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2',
'param3', 'param4', 'measurement_csd'
]
cart = np.array([data['x'], data['y'], -data['negz']]).transpose()
dir = pmag.cart2dir(cart).transpose()
data['measurement_dec'] = dir[0]
data['measurement_inc'] = dir[1]
data['measurement_magn_moment'] = dir[2] * (
10.0**
data['expon']) * volume # the data are in A/m - this converts to Am^2
data['measurement_magn_volume'] = dir[2] * (10.0**data['expon']
) # A/m - data in A/m
data['sample_dip'] = -data['sample_dip']
DGEOs, IGEOs = [], []
for ind in range(len(data)):
dgeo, igeo = pmag.dogeo(data.iloc[ind]['measurement_dec'],
data.iloc[ind]['measurement_inc'],
data.iloc[ind]['sample_azimuth'],
data.iloc[ind]['sample_dip'])
DGEOs.append(dgeo)
IGEOs.append(igeo)
data['specimen_dec'] = DGEOs
data['specimen_inc'] = IGEOs
data['specimen_tilt'] = '1'
if specnum != 0:
data['er_sample_name'] = data['er_specimen_name'][:specnum]
else:
data['er_sample_name'] = data['er_specimen_name']
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
data['er_site_name'] = pmag.parse_site(data['er_sample_name'],
samp_con, Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# Configure the er_sample table
for rowNum, row in data.iterrows():
sampleFlag = 0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == row['er_sample_name']:
sampleFlag = 1
break
if sampleFlag == 0:
ErSampRec['er_sample_name'] = row['er_sample_name']
ErSampRec['sample_azimuth'] = str(row['sample_azimuth'])
ErSampRec['sample_dip'] = str(row['sample_dip'])
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = row['er_site_name']
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
# MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = row['er_site_name']
MagRec['er_sample_name'] = row['er_sample_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["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = row['er_specimen_name']
MagRec["treatment_ac_field"] = '0'
if row['step'] == 'NRM':
meas_type = "LT-NO"
elif row['step'][0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(row['step'][2:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type = "LT-T-Z"
treat = float(row['step'][2:])
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MagRec["measurement_magn_moment"] = str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"] = str(row['measurement_magn_volume'])
MagRec["measurement_dec"] = str(row['measurement_dec'])
MagRec["measurement_inc"] = str(row['measurement_inc'])
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print("sample orientations put in ", samp_file)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
print("exit!")
return True, meas_file
def main():
"""
NAME
mini_magic.py
DESCRIPTION
converts the Yale minispin format to magic_measurements format files
SYNTAX
mini_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, required
-F FILE: specify output file, default is magic_measurements.txt
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
-vol: volume assumed for measurement in cm^3
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
[10] LL-SI-SA-SP_STEP where LL is location, SI is site, SA is sample and SP is specimen and STEP is demagnetization step
INPUT
Must put separate experiments (all AF, thermal, etc.) in
seperate files
Format of Yale MINI files:
LL-SI-SP_STEP, Declination, Inclination, Intensity (mA/m), X,Y,Z
"""
# initialize some stuff
noave=0
methcode,inst="LP-NO",""
samp_con,Z='10',1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
coil=""
volume=10e-6 # assume a volume of 10cc
#
# get command line arguments
#
user=""
dir_path='./'
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+args[ind+1]
else:
meas_file=dir_path+'magic_measurements.txt'
if '-f' in args:
ind=args.index("-f")
magfile=dir_path+args[ind+1]
try:
input=open(magfile,'r')
except:
print("bad mag file name")
sys.exit()
else:
print("mag_file field is required option")
print(main.__doc__)
sys.exit()
specnum=0
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 "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-vol" in args:
ind=args.index("-vol")
volume=1e-6*float(args[ind+1])
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'
methcode="LT-AF-Z"
if "T" in codes:
demag="T"
MagRecs=[]
version_num=pmag.get_version()
for line in input.readlines():
rec=line.split(',')
if len(rec)>1:
MagRec={}
IDs=rec[0].split('_')
treat=IDs[1]
MagRec["er_specimen_name"]=IDs[0]
print(MagRec['er_specimen_name'])
sids=IDs[0].split('-')
MagRec['er_location_name']=sids[0]
MagRec['er_site_name']=sids[0]+'-'+sids[1]
if len(sids)==2:
MagRec["er_sample_name"]=IDs[0]
else:
MagRec["er_sample_name"]=sids[0]+'-'+sids[1]+'-'+sids[2]
print(MagRec)
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"
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(treat)*1e-3) # peak field in tesla
if demag=="T":
meas_type="LT-T-Z"
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_temp"]='%8.3e' % (float(treat)+273.) # temp in kelvin
if demag=="N":
meas_type="LT-NO"
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["measurement_magn_moment"]='%10.3e'% (volume*float(rec[3])*1e-3) # moment in Am2 (from mA/m)
MagRec["measurement_dec"]=rec[1]
MagRec["measurement_inc"]=rec[2]
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=methcode.strip(':')
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print("results put in ",meas_file)
def main(command_line=True, **kwargs):
"""
NAME
_2g_bin_magic.py
DESCRIPTION
takes the binary 2g format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2g_bin_magic.py [command line options]
OPTIONS
-f FILE: specify input 2g (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sites.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
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 = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
mag_file = ''
specnum = 0
ub_file, samp_file, or_con, corr, meas_file = "", "er_samples.txt", "3", "1", "magic_measurements.txt"
pos_file, site_file = "", "er_sites.txt"
noave = 1
args = sys.argv
bed_dip, bed_dip_dir = "", ""
samp_con, Z, average_bedding = "2", 1, "0"
meths = 'FS-FD'
sclass, lithology, _type = "", "", ""
user, inst = "", ""
DecCorr = 0.
location_name = "unknown"
months = [
'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct',
'Nov', 'Dec'
]
gmeths = ""
#
#
dir_path = '.'
if command_line:
if '-WD' in args:
ind = args.index("-WD")
dir_path = sys.argv[ind + 1]
if "-h" in args:
print(main.__doc__)
return False
if "-f" in args:
ind = args.index("-f")
mag_file = sys.argv[ind + 1]
if "-fpos" in args:
ind = args.index("-fpos")
pos_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = sys.argv[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = sys.argv[ind + 1]
if "-Fsi" in args:
ind = args.index("-Fsi")
site_file = sys.argv[ind + 1]
if "-ocn" in args:
ind = args.index("-ocn")
or_con = sys.argv[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "-mcd" in args:
ind = args.index("-mcd")
gmeths = (sys.argv[ind + 1])
if "-loc" in args:
ind = args.index("-loc")
location_name = (sys.argv[ind + 1])
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-a" in args:
noave = 0
#
ID = False
if '-ID' in args:
ind = args.index('-ID')
ID = args[ind + 1]
#
if not command_line:
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
pos_file = kwargs.get('pos_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', '')
location_name = kwargs.get('location_name', '')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 1) # default is DO average
ID = kwargs.get('ID', '')
# format and fix variables acquired from command line args or input with **kwargs
if specnum != 0: specnum = -specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
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")
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 "6" in samp_con:
try:
Samps, file_type = pmag.magic_read(
os.path.join(input_dir_path, 'er_samples.txt'))
except:
print(
"there is no er_samples.txt file in your input directory - you can't use naming convention #6"
)
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if file_type == 'bad_file':
print(
"there is no er_samples.txt file in your input directory - you can't use naming convention #6"
)
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if not mag_file:
print("mag file is required input")
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = output_dir_path + '/' + samp_file
site_file = output_dir_path + '/' + site_file
meas_file = output_dir_path + '/' + meas_file
samplist = []
try:
Samps, file_type = pmag.magic_read(samp_file)
for samp in Samps:
if samp['er_sample_name'] not in samplist:
samplist.append(samp['er_sample_name'])
except:
Samps = []
MagRecs = []
try:
f = open(mag_file, 'brU')
input = str(f.read()).strip("b '")
f.close()
except Exception as ex:
print('ex', ex)
print("bad mag file")
return False, "bad mag file"
firstline, date = 1, ""
d = input.split('\\xcd')
for line in d:
rec = line.split('\\x00')
if firstline == 1:
firstline = 0
spec, vol = "", 1
el = 51
while line[el:el + 1] != "\\":
spec = spec + line[el]
el += 1
# check for bad sample name
test = spec.split('.')
date = ""
if len(test) > 1:
spec = test[0]
kk = 24
while line[kk] != '\\x01' and line[kk] != '\\x00':
kk += 1
vcc = line[24:kk]
el = 10
while rec[el].strip() != '':
el += 1
date, comments = rec[el + 7], []
else:
el = 9
while rec[el] != '\\x01':
el += 1
vcc, date, comments = rec[el - 3], rec[el + 7], []
specname = spec.lower()
print('importing ', specname)
el += 8
while rec[el].isdigit() == False:
comments.append(rec[el])
el += 1
while rec[el] == "":
el += 1
az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
pl = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip_dir = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip = float(rec[el])
el += 1
while rec[el] == "":
el += 1
if rec[el] == '\\x01':
bed_dip = 180. - bed_dip
el += 1
while rec[el] == "":
el += 1
fold_az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
fold_pl = rec[el]
el += 1
while rec[el] == "":
el += 1
if rec[el] != "" and rec[el] != '\\x02' and rec[el] != '\\x01':
deccorr = float(rec[el])
az += deccorr
bed_dip_dir += deccorr
fold_az += deccorr
if bed_dip_dir >= 360: bed_dip_dir = bed_dip_dir - 360.
if az >= 360.: az = az - 360.
if fold_az >= 360.: fold_az = fold_az - 360.
else:
deccorr = 0
if specnum != 0:
sample = specname[:specnum]
else:
sample = specname
SampRec = {}
SampRec["er_sample_name"] = sample
SampRec["er_location_name"] = location_name
SampRec["er_citation_names"] = "This study"
labaz, labdip = pmag.orient(az, pl,
or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"] = '%7.1f' % (bed_dip)
SampRec["sample_bed_dip_direction"] = '%7.1f' % (bed_dip_dir)
SampRec["sample_dip"] = '%7.1f' % (labdip)
SampRec["sample_azimuth"] = '%7.1f' % (labaz)
if vcc.strip() != "":
vol = float(vcc) * 1e-6 # convert to m^3 from cc
SampRec["sample_volume"] = '%10.3e' % (vol) #
SampRec["sample_class"] = sclass
SampRec["sample_lithology"] = lithology
SampRec["sample_type"] = _type
SampRec["sample_declination_correction"] = '%7.1f' % (deccorr)
methods = gmeths.split(':')
if deccorr != "0":
if 'SO-MAG' in methods: del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths = ""
for meth in methods:
meths = meths + meth + ":"
meths = meths[:-1]
SampRec["magic_method_codes"] = meths
if int(samp_con) < 6 or int(samp_con) == 7:
site = pmag.parse_site(SampRec["er_sample_name"], samp_con,
Z) # parse out the site name
SampRec["er_site_name"] = site
elif len(Samps) > 1:
site, location = "", ""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site = samp["er_site_name"]
location = samp["er_location_name"]
break
SampRec["er_location_name"] = samp["er_location_name"]
SampRec["er_site_name"] = samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
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"] = specname
MagRec["er_sample_name"] = SampRec['er_sample_name']
MagRec["er_site_name"] = SampRec['er_site_name']
MagRec["er_location_name"] = location_name
el, demag = 1, ''
treat = rec[el]
if treat[-1] == 'C':
demag = 'T'
elif treat != 'NRM':
demag = 'AF'
el += 1
while rec[el] == "":
el += 1
MagRec["measurement_dec"] = rec[el]
cdec = float(rec[el])
el += 1
while rec[el] == "":
el += 1
MagRec["measurement_inc"] = rec[el]
cinc = float(rec[el])
el += 1
while rec[el] == "":
el += 1
gdec = rec[el]
el += 1
while rec[el] == "":
el += 1
ginc = rec[el]
el = skip(2, el, rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"] = '%10.3e' % (
float(rec[el]) * 1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"] = '%10.3e' % (
float(rec[el]) * 1e-3 / vol) # magnetization in A/m
el = skip(2, el, rec) # skip to xsig
MagRec["measurement_sd_x"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to ysig
MagRec["measurement_sd_y"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to zsig
MagRec["measurement_sd_z"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el += 1 # skip to positions
MagRec["measurement_positions"] = rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"] = inst
MagRec["er_analyst_mail_names"] = ""
MagRec["er_citation_names"] = "This study"
MagRec["magic_method_codes"] = meas_type
if demag == "AF":
MagRec["treatment_ac_field"] = '%8.3e' % (
float(treat[:-2]) * 1e-3) # peak field in tesla
meas_type = "LT-AF-Z"
MagRec["treatment_dc_field"] = '0'
elif demag == "T":
MagRec["treatment_temp"] = '%8.3e' % (float(treat[:-1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
MagOuts, keylist = pmag.fillkeys(MagOuts)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("Measurements put in ", meas_file)
SampsOut, sampkeys = pmag.fillkeys(Samps)
pmag.magic_write(samp_file, SampsOut, "er_samples")
Sites = []
for samp in Samps:
SiteRec = {}
SiteRec['er_site_name'] = samp['er_site_name']
SiteRec['er_location_name'] = samp['er_location_name']
SiteRec['site_definition'] = 's'
SiteRec['er_citation_names'] = 'This study'
if 'sample_class' in list(samp.keys()):
SiteRec['site_class'] = samp['sample_class']
if 'sample_lithology' in list(samp.keys()):
SiteRec['site_lithology'] = samp['sample_lithology']
if 'sample_type' in list(samp.keys()):
SiteRec['site_lithology'] = samp['sample_lithology']
if 'sample_lat' in list(samp.keys()):
SiteRec['site_lat'] = samp['sample_lat']
else:
SiteRec['site_lat'] = "-999"
if 'sample_lon' in list(samp.keys()):
SiteRec['site_lon'] = samp['sample_lon']
else:
SiteRec['site_lon'] = "-999"
if 'sample_height' in list(samp.keys()):
SiteRec['site_height'] = samp['sample_height']
Sites.append(SiteRec)
pmag.magic_write(site_file, Sites, 'er_sites')
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
iodp_dscr_magic.py
DESCRIPTION
converts ODP LIMS discrete sample format files to magic_measurements format files
SYNTAX
iodp_descr_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-A : don't average replicate measurements
INPUTS
IODP discrete sample .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
csv_file=''
MagRecs,Specs=[],[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
# get command line args
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
csv_file=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
# format variables
meas_file= os.path.join(output_dir_path, meas_file)
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist=[csv_file]
# parsing the data
file_found = False
for fname in filelist: # parse each file
if fname[-3:].lower()=='csv':
file_found = True
print('processing: ',fname)
with open(fname, 'r') as finput:
data = list(finput.readlines())
keys = data[0].replace('\n','').split(',') # splits on underscores
interval_key="Offset (cm)"
demag_key="Demag level (mT)"
offline_demag_key="Treatment Value (mT or °C)"
offline_treatment_type="Treatment type"
run_key="Test No."
if "Inclination background + tray corrected (deg)" in keys: inc_key="Inclination background + tray corrected (deg)"
if "Inclination background & tray corrected (deg)" in keys: inc_key="Inclination background & tray corrected (deg)"
if "Declination background + tray corrected (deg)" in keys: dec_key="Declination background + tray corrected (deg)"
if "Declination background & tray corrected (deg)" in keys: dec_key="Declination background & tray corrected (deg)"
if "Intensity background + tray corrected (A/m)" in keys: int_key="Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys: int_key="Intensity background & tray corrected (A/m)"
type="Type"
sect_key="Sect"
half_key="A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:volume_key="Sample volume (cm^3)"
if "Sample volume (cc)" in keys:volume_key="Sample volume (cc)"
if "Sample volume (cm³)" in keys:volume_key="Sample volume (cm³)"
for line in data[1:]:
InRec={}
for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k]
inst="IODP-SRM"
MagRec={}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
offsets=InRec[interval_key].split('.') # maintain consistency with er_samples convention of using top interval
if len(offsets)==1:
offset=int(offsets[0])
else:
offset=int(offsets[0])-1
#interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval=str(offset)# maintain consistency with er_samples convention of using top interval
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"-"+InRec[sect_key]+'_'+InRec[half_key]+'_'+interval
if specimen not in Specs:Specs.append(specimen)
MagRec['er_expedition_name']=expedition
MagRec['er_location_name']=location
MagRec['er_site_name']=specimen
MagRec['er_citation_names']=citation
MagRec['er_specimen_name']=specimen
MagRec['er_sample_name']=specimen
MagRec['er_site_name']=specimen
# set up measurement record - default is NRM
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='0' # assume all data are "good"
volume=InRec[volume_key]
MagRec["magic_method_codes"]='LT-NO'
sort_by='treatment_ac_field' # set default to AF demag
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
if sort_by =="treatment_ac_field":
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
else:
MagRec["treatment_ac_field"]=str(treatment_value)# AF demag in treat mT => T
elif offline_treatment_type in list(InRec.keys()) and InRec[offline_treatment_type]!="":
if "Lowrie" in InRec['Comments']:
MagRec['magic_method_codes'] = 'LP-IRM-3D'
treatment_value=float(InRec[offline_demag_key].strip('"'))+273. # convert C => K
MagRec["treatment_temp"]=treatment_value
MagRec["treatment_ac_field"]="0"
sort_by='treatment_temp'
elif 'Isothermal' in InRec[offline_treatment_type]:
MagRec['magic_method_codes'] = 'LT-IRM'
treatment_value=float(InRec[offline_demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_dc_field"]=treatment_value
MagRec["treatment_ac_field"]="0"
sort_by='treatment_dc_field'
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_key in list(InRec.keys()):
run_number=InRec[run_key]
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
MagRec['measurement_description']='sample orientation: '+InRec['Sample orientation']
MagRec['measurement_inc']=InRec[inc_key].strip('"')
MagRec['measurement_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
MagOuts=[]
for spec in Specs:
Speclist=pmag.get_dictitem(MagRecs,'er_specimen_name',spec,'T')
Meassorted=sorted(Speclist, key=lambda x,y=None: int(round(float(x[sort_by])-float(y[sort_by]))) if y!=None else 0)
for rec in Meassorted:
for key in list(rec.keys()): rec[key]=str(rec[key])
MagOuts.append(rec)
Fixed=pmag.measurements_methods(MagOuts,noave)
Out,keys=pmag.fillkeys(Fixed)
if pmag.magic_write(meas_file,Out,'magic_measurements'):
print('data stored in ',meas_file)
return True, meas_file
else:
print('no data found. bad magfile?')
return False, 'no data found. bad magfile?'
def main(command_line=True, **kwargs):
"""
NAME
iodp_dscr_magic.py
DESCRIPTION
converts ODP LIMS discrete sample format files to magic_measurements format files
SYNTAX
iodp_descr_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-A : don't average replicate measurements
INPUTS
IODP discrete sample .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num = pmag.get_version()
meas_file = 'magic_measurements.txt'
csv_file = ''
MagRecs, Specs = [], []
citation = "This study"
dir_path, demag = '.', 'NRM'
args = sys.argv
noave = 0
# get command line args
if command_line:
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if "-A" in args: noave = 1
if '-f' in args:
ind = args.index("-f")
csv_file = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
# format variables
meas_file = os.path.join(output_dir_path, meas_file)
if csv_file == "":
filelist = os.listdir(
input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist = [csv_file]
# parsing the data
file_found = False
for fname in filelist: # parse each file
if fname[-3:].lower() == 'csv':
file_found = True
print('processing: ', fname)
with open(fname, 'r') as finput:
data = list(finput.readlines())
keys = data[0].replace('\n',
'').split(',') # splits on underscores
interval_key = "Offset (cm)"
demag_key = "Demag level (mT)"
offline_demag_key = "Treatment Value (mT or °C)"
offline_treatment_type = "Treatment type"
run_key = "Test No."
if "Inclination background + tray corrected (deg)" in keys:
inc_key = "Inclination background + tray corrected (deg)"
if "Inclination background & tray corrected (deg)" in keys:
inc_key = "Inclination background & tray corrected (deg)"
if "Declination background + tray corrected (deg)" in keys:
dec_key = "Declination background + tray corrected (deg)"
if "Declination background & tray corrected (deg)" in keys:
dec_key = "Declination background & tray corrected (deg)"
if "Intensity background + tray corrected (A/m)" in keys:
int_key = "Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys:
int_key = "Intensity background & tray corrected (A/m)"
type = "Type"
sect_key = "Sect"
half_key = "A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:
volume_key = "Sample volume (cm^3)"
if "Sample volume (cc)" in keys: volume_key = "Sample volume (cc)"
if "Sample volume (cm³)" in keys:
volume_key = "Sample volume (cm³)"
for line in data[1:]:
InRec = {}
for k in range(len(keys)):
InRec[keys[k]] = line.split(',')[k]
inst = "IODP-SRM"
MagRec = {}
expedition = InRec['Exp']
location = InRec['Site'] + InRec['Hole']
offsets = InRec[interval_key].split(
'.'
) # maintain consistency with er_samples convention of using top interval
if len(offsets) == 1:
offset = int(offsets[0])
else:
offset = int(offsets[0]) - 1
#interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval = str(
offset
) # maintain consistency with er_samples convention of using top interval
specimen = expedition + '-' + location + '-' + InRec[
'Core'] + InRec[type] + "-" + InRec[
sect_key] + '_' + InRec[half_key] + '_' + interval
if specimen not in Specs: Specs.append(specimen)
MagRec['er_expedition_name'] = expedition
MagRec['er_location_name'] = location
MagRec['er_site_name'] = specimen
MagRec['er_citation_names'] = citation
MagRec['er_specimen_name'] = specimen
MagRec['er_sample_name'] = specimen
MagRec['er_site_name'] = specimen
# set up measurement record - default is NRM
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'
MagRec["measurement_flag"] = 'g' # assume all data are "good"
MagRec[
"measurement_standard"] = 'u' # assume all data are "good"
MagRec["measurement_csd"] = '0' # assume all data are "good"
volume = InRec[volume_key]
MagRec["magic_method_codes"] = 'LT-NO'
sort_by = 'treatment_ac_field' # set default to AF demag
if InRec[demag_key] != "0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value = float(
InRec[demag_key].strip('"')) * 1e-3 # convert mT => T
if sort_by == "treatment_ac_field":
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
else:
MagRec["treatment_ac_field"] = str(
treatment_value) # AF demag in treat mT => T
elif offline_treatment_type in list(
InRec.keys()) and InRec[offline_treatment_type] != "":
if "Lowrie" in InRec['Comments']:
MagRec['magic_method_codes'] = 'LP-IRM-3D'
treatment_value = float(InRec[offline_demag_key].strip(
'"')) + 273. # convert C => K
MagRec["treatment_temp"] = treatment_value
MagRec["treatment_ac_field"] = "0"
sort_by = 'treatment_temp'
elif 'Isothermal' in InRec[offline_treatment_type]:
MagRec['magic_method_codes'] = 'LT-IRM'
treatment_value = float(InRec[offline_demag_key].strip(
'"')) * 1e-3 # convert mT => T
MagRec["treatment_dc_field"] = treatment_value
MagRec["treatment_ac_field"] = "0"
sort_by = 'treatment_dc_field'
MagRec[
"measurement_standard"] = 'u' # assume all data are "good"
vol = float(volume) * 1e-6 # convert from cc to m^3
if run_key in list(InRec.keys()):
run_number = InRec[run_key]
MagRec['external_database_ids'] = run_number
MagRec['external_database_names'] = 'LIMS'
else:
MagRec['external_database_ids'] = ""
MagRec['external_database_names'] = ''
MagRec[
'measurement_description'] = 'sample orientation: ' + InRec[
'Sample orientation']
MagRec['measurement_inc'] = InRec[inc_key].strip('"')
MagRec['measurement_dec'] = InRec[dec_key].strip('"')
intens = InRec[int_key].strip('"')
MagRec['measurement_magn_moment'] = '%8.3e' % (
float(intens) * vol
) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes'] = inst
MagRec['measurement_number'] = '1'
MagRec['measurement_positions'] = ''
MagRecs.append(MagRec)
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
MagOuts = []
for spec in Specs:
Speclist = pmag.get_dictitem(MagRecs, 'er_specimen_name', spec, 'T')
Meassorted = sorted(Speclist,
key=lambda x, y=None: int(
round(float(x[sort_by]) - float(y[sort_by])))
if y != None else 0)
for rec in Meassorted:
for key in list(rec.keys()):
rec[key] = str(rec[key])
MagOuts.append(rec)
Fixed = pmag.measurements_methods(MagOuts, noave)
Out, keys = pmag.fillkeys(Fixed)
if pmag.magic_write(meas_file, Out, 'magic_measurements'):
print('data stored in ', meas_file)
return True, meas_file
else:
print('no data found. bad magfile?')
return False, 'no data found. bad magfile?'
def main(command_line=True, **kwargs):
"""
NAME
ldeo_magic.py
DESCRIPTION
converts LDEO format files to magic_measurements format files
SYNTAX
ldeo_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .ldeo format input file, required
-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)
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
-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
-ARM_dc # default value is 50e-6
-ARM_temp # default is 600c
-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
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 LDEO files:
isaf2.fix
LAT: .00 LON: .00
ID TREAT I CD J CDECL CINCL GDECL GINCL BDECL BINCL SUSC M/V
________________________________________________________________________________
is031c2 .0 SD 0 461.600 163.9 17.5 337.1 74.5 319.1 74.4 .0 .0
ID: specimen name
TREAT: treatment step
I: Instrument
CD: Circular standard devation
J: intensity. assumed to be total moment in 10^-4 (emu)
CDECL: Declination in specimen coordinate system
CINCL: Declination in specimen coordinate system
GDECL: Declination in geographic coordinate system
GINCL: Declination in geographic coordinate system
BDECL: Declination in bedding adjusted coordinate system
BINCL: Declination in bedding adjusted coordinate system
SUSC: magnetic susceptibility (in micro SI)a
M/V: mass or volume for nomalizing (0 won't normalize)
"""
# initialize some stuff
noave = 0
codelist = ''
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'
magfile = ''
trm = 0
irm = 0
specnum = 0
coil = ""
arm_labfield = 50e-6
trm_peakT = 600 + 273
#
# get command line arguments
#
meas_file = "magic_measurements.txt"
user = ""
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")
magfile = 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 '-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]
if '-ARM_dc' in args:
ind = args.index("-ARM_dc")
arm_labfield = args[ind + 1]
if '-ARM_temp' in args:
ind = args.index('-ARM_temp')
trm_peakT = args[ind + 1]
if not command_line:
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
synfile = kwargs.get('synfile', 'er_synthetics.txt')
# rm samp_file = kwargs.get('samp_file', '')
magfile = kwargs.get('magfile', '')
labfield = int(kwargs.get('labfield', 0)) * 1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = int(kwargs.get('peakfield', 0)) * 1e-3
specnum = int(kwargs.get('specnum', 0))
er_location_name = kwargs.get('er_location_name', '')
# rm 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) # 0 means "do average", is default
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
arm_labfield = kwargs.get('arm_labfield', 50e-6)
trm_peakT = kwargs.get('trm_peakT', 600 + 273)
# format/organize variables
if magfile:
try:
input = open(magfile, 'r')
except:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
print(main.__doc__)
return False, "mag_file field is required option"
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print(
"naming convention 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"
if "7" in samp_con:
if "-" not in samp_con:
print(
"naming convention 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 = "4"
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
if not labfield: methcode = "LT-AF-Z"
if labfield: methcode = "LT-AF-I"
if "T" in codes:
demag = "T"
if not labfield: methcode = "LT-T-Z"
if labfield: methcode = "LT-T-I"
if "I" in codes:
methcode = "LP-IRM"
irmunits = "mT"
if "S" in codes:
demag = "S"
methcode = "LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield = labfield
# should use arm_labfield and trm_peakT as well, but these values are currently never asked for
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 coil:
methcode = "LP-IRM"
irmunits = "V"
if coil not in ["1", "2", "3"]:
print(main.__doc__)
print('not a valid coil specification')
return False, 'not a valid coil specification'
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 1: # ldeo file format
#
# find start of data:
#
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_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["measurement_chi"] = '%10.3e' % (
float(rec[11]) * 1e-5
) #convert to SI (assume Bartington, 10-5 SI)
#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 len(SynRecs) > 0:
pmag.magic_write(synfile, SynRecs, 'er_synthetics')
print("synthetics put in ", synfile)
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
pmd_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
pmd_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-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
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
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.
INPUT
PMD format files
"""
# initialize some stuff
noave = 0
inst = ""
samp_con, Z = '1', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
specnum = -1
MagRecs = []
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
DIspec = []
MagFiles = []
user = ""
mag_file = ""
dir_path = '.'
ErSamps = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
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]
#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 = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args: noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path + "/" + mag_file
meas_file = output_dir_path + "/" + meas_file
samp_file = output_dir_path + "/" + samp_file
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention 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"
if "7" in samp_con:
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"
# parse data
data = open(mag_file, 'rU').readlines() # read in data from file
comment = data[0]
line = data[1].strip()
line = line.replace("=", "= ") # make finding orientations easier
rec = line.split() # read in sample orientation, etc.
er_specimen_name = rec[0]
ErSampRec, ErSiteRec = {}, {} # make a sample record
if specnum != 0:
er_sample_name = rec[0][:specnum]
else:
er_sample_name = rec[0]
if len(ErSamps) > 0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name'] == er_sample_name:
ErSampRec = samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con) < 6:
er_site_name = pmag.parse_site(er_sample_name, samp_con, Z)
else:
if 'er_site_name' in ErSampRec.keys():
er_site_name = ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():
er_location_name = ErSampREc['er_location_name']
az_ind = rec.index('a=') + 1
ErSampRec['er_sample_name'] = er_sample_name
ErSampRec['er_sample_description'] = comment
ErSampRec['sample_azimuth'] = rec[az_ind]
dip_ind = rec.index('b=') + 1
dip = -float(rec[dip_ind])
ErSampRec['sample_dip'] = '%7.1f' % (dip)
strike_ind = rec.index('s=') + 1
ErSampRec['sample_bed_dip_direction'] = '%7.1f' % (float(rec[strike_ind]) +
90.)
bd_ind = rec.index('d=') + 1
ErSampRec['sample_bed_dip'] = rec[bd_ind]
v_ind = rec.index('v=') + 1
vol = rec[v_ind][:-3]
date = rec[-2]
time = rec[-1]
ErSampRec['magic_method_codes'] = meth_code
if 'er_location_name' not in ErSampRec.keys():
ErSampRec['er_location_name'] = er_location_name
if 'er_site_name' not in ErSampRec.keys():
ErSampRec['er_site_name'] = er_site_name
if 'er_citation_names' not in ErSampRec.keys():
ErSampRec['er_citation_names'] = 'This study'
if 'magic_method_codes' not in ErSampRec.keys():
ErSampRec['magic_method_codes'] = 'SO-NO'
SampOuts.append(ErSampRec)
for k in range(3, len(data)): # read in data
line = data[k]
rec = line.split()
if len(rec) > 1: # skip blank lines at bottom
MagRec = {}
MagRec['measurement_description'] = 'Date: ' + date + ' ' + time
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = er_sample_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["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = er_specimen_name
if rec[0] == 'NRM':
meas_type = "LT-NO"
elif rec[0][0] == 'M' or rec[0][0] == 'H':
meas_type = "LT-AF-Z"
elif rec[0][0] == 'T':
meas_type = "LT-T-Z"
else:
print "measurement type unknown"
return False, "measurement type unknown"
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MagRec["measurement_magn_moment"] = '%10.3e' % (Vec[2]) # Am^2
MagRec["measurement_magn_volume"] = rec[4] # A/m
MagRec["measurement_dec"] = '%7.1f' % (Vec[0])
MagRec["measurement_inc"] = '%7.1f' % (Vec[1])
MagRec["treatment_ac_field"] = '0'
if meas_type != 'LT-NO':
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
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, SampOuts, 'er_samples')
print "sample orientations put in ", samp_file
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
ldeo_magic.py
DESCRIPTION
converts LDEO format files to magic_measurements format files
SYNTAX
ldeo_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .ldeo format input file, required
-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)
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
-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
-ARM_dc # default value is 50e-6
-ARM_temp # default is 600c
-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
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 LDEO files:
isaf2.fix
LAT: .00 LON: .00
ID TREAT I CD J CDECL CINCL GDECL GINCL BDECL BINCL SUSC M/V
________________________________________________________________________________
is031c2 .0 SD 0 461.600 163.9 17.5 337.1 74.5 319.1 74.4 .0 .0
ID: specimen name
TREAT: treatment step
I: Instrument
CD: Circular standard devation
J: intensity. assumed to be total moment in 10^-4 (emu)
CDECL: Declination in specimen coordinate system
CINCL: Declination in specimen coordinate system
GDECL: Declination in geographic coordinate system
GINCL: Declination in geographic coordinate system
BDECL: Declination in bedding adjusted coordinate system
BINCL: Declination in bedding adjusted coordinate system
SUSC: magnetic susceptibility (in micro SI)a
M/V: mass or volume for nomalizing (0 won't normalize)
"""
# initialize some stuff
noave=0
codelist = ''
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'
magfile = ''
trm=0
irm=0
specnum=0
coil=""
arm_labfield = 50e-6
trm_peakT = 600+273
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
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")
magfile=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 '-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]
if '-ARM_dc' in args:
ind = args.index("-ARM_dc")
arm_labfield = args[ind+1]
if '-ARM_temp' in args:
ind = args.index('-ARM_temp')
trm_peakT = args[ind+1]
if not command_line:
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
synfile = kwargs.get('synfile', 'er_synthetics.txt')
# rm samp_file = kwargs.get('samp_file', '')
magfile = kwargs.get('magfile', '')
labfield = int(kwargs.get('labfield', 0)) *1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = int(kwargs.get('peakfield', 0))*1e-3
specnum = int(kwargs.get('specnum', 0))
er_location_name = kwargs.get('er_location_name', '')
# rm 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) # 0 means "do average", is default
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
arm_labfield = kwargs.get('arm_labfield', 50e-6)
trm_peakT = kwargs.get('trm_peakT', 600+273)
# format/organize variables
if magfile:
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
return False, "bad mag file name"
else:
print "mag_file field is required option"
print main.__doc__
return False, "mag_file field is required option"
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention 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"
if "7" in samp_con:
if "-" not in samp_con:
print "naming convention 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="4"
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if not labfield: methcode="LT-AF-Z"
if labfield: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if not labfield: methcode="LT-T-Z"
if labfield: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
# should use arm_labfield and trm_peakT as well, but these values are currently never asked for
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 coil:
methcode="LP-IRM"
irmunits="V"
if coil not in ["1","2","3"]:
print main.__doc__
print 'not a valid coil specification'
return False, 'not a valid coil specification'
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 1: # ldeo file format
#
# find start of data:
#
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_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["measurement_chi"]='%10.3e'%(float(rec[11])*1e-5)#convert to SI (assume Bartington, 10-5 SI)
#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 len(SynRecs)>0:
pmag.magic_write(synfile,SynRecs,'er_synthetics')
print "synthetics put in ",synfile
return True, meas_file
def main(command_line=True, **kwargs):
"""
NAME
bgc_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
bgc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume in cc of the sample, default 2.5^3cc. Will use vol in data file if volume!=0 in file.
INPUT
BGC paleomag format file
"""
# initialize some stuff
noave = 0
volume = 0.025**3 #default volume is a 2.5cm cube
#inst=""
#samp_con,Z='1',""
#missing=1
#demag="N"
er_location_name = "unknown"
er_site_name = "unknown"
#citation='This study'
args = sys.argv
meth_code = "LP-NO"
#specnum=1
version_num = pmag.get_version()
mag_file = ""
dir_path = '.'
MagRecs = []
SampOuts = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
meth_code = ""
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
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]
#try:
# open(samp_file,'r')
# 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 = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind+1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind+1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind+1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind+1]
#samp_con='5'
if "-v" in args:
ind = args.index("-v")
volume = float(args[ind+1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
er_location_name = kwargs.get('er_location_name', '')
er_site_name = kwargs.get('er_site_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
# format variables
if not mag_file:
return False, 'You must provide a BCG format file'
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
sample_name = line_items[2]
sample_name = sample_name.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
sample_azimuth = float(line_items[1])
sample_dip = float(line_items[2])
sample_bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
sample_lon = line_items[5]
sample_lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['measurement_dec'] = direction[0]
data['measurement_inc'] = direction[1]
data['measurement_magn_moment'] = old_div(direction[2], 1000) # the data are in EMU - this converts to Am^2
data['measurement_magn_volume'] = old_div((old_div(direction[2], 1000)), volume) # EMU - data converted to A/m
# Configure the er_sample table
ErSampRec['er_sample_name'] = sample_name
ErSampRec['sample_azimuth'] = sample_azimuth
ErSampRec['sample_dip'] = sample_dip
ErSampRec['sample_bed_dip_direction'] = sample_bed_azimuth
ErSampRec['sample_bed_dip'] = sample_bed_dip
ErSampRec['sample_lat'] = sample_lat
ErSampRec['sample_lon'] = sample_lon
ErSampRec['magic_method_codes'] = meth_code
ErSampRec['er_location_name'] = er_location_name
ErSampRec['er_site_name'] = er_site_name
ErSampRec['er_citation_names'] = 'This study'
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
MagRec['measurement_description'] = 'Date: ' + str(row['Date']) + ' Time: ' + str(row['Time'])
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['er_site_name'] = er_site_name
MagRec['er_sample_name'] = sample_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["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = rowNum
MagRec["er_specimen_name"] = sample_name
MagRec["treatment_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MagRec["treatment_ac_field"] = '%8.3e' %(treat*1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MagRec["treatment_temp"] = '%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ", rowNum)
MagRec["measurement_magn_moment"] = str(row['measurement_magn_moment'])
MagRec["measurement_magn_volume"] = str(row['measurement_magn_volume'])
MagRec["measurement_dec"] = str(row['measurement_dec'])
MagRec["measurement_inc"] = str(row['measurement_inc'])
MagRec['magic_method_codes'] = meas_type
MagRec['measurement_csd'] = '0.0' # added due to magic.write error
MagRec['measurement_positions'] = '1' # added due to magic.write error
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, 'er_samples')
print("sample orientations put in ", samp_file)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print("results put in ", meas_file)
return True, meas_file
def main():
"""
NAME
odp_spn_magic.py
DESCRIPTION
converts ODP's Molspin's .spn format files to magic_measurements format files
SYNTAX
odp_spn_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify .spn format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-LP [AF, T, A FIELD, I N] specify one (FIELD is DC field in uT)
AF: af demag
T: thermal
A: anhysteretic remanence
I: isothermal remanence
N: NRM only
-v vol , specify volume used in MolSpin program in cm^3
-A: don't average replicate measurements
INPUT
Best to put separate experiments (all AF, thermal, ARM, etc. files in
seperate .spn files
Format of .spn files:
header with:
Leg Sit H Cor T Sec Top Bot Dec Inc Intens Demag. Stage
followed by data
Leg: Expedition number
Sit: is ODP Site
H: Hole letter
Cor: Core number
T: Core type (R,H,X,etc.)
Sec: section number
top: top of sample interval
bot: bottom of sample interval
Intens in mA/m
Demag Stage:
XXX T in Centigrade
XXX AF in mT
"""
# initialize some stuff
noave = 0
methcode, inst = "", ""
phi, theta, peakfield, labfield = 0, 0, 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]
missing = 1
demag = "N"
er_location_name = ""
citation = 'This study'
args = sys.argv
methcode = "LP-NO"
trm = 0
irm = 0
dc = "0"
dir_path = '.'
#
# get command line arguments
#
meas_file = "magic_measurements.txt"
user = ""
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
samp_file = dir_path + '/' + 'er_samples.txt'
if "-h" in args:
print main.__doc__
sys.exit()
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-f' in args:
ind = args.index("-f")
mag_file = dir_path + '/' + args[ind + 1]
try:
input = open(mag_file, 'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "spn_file field is required option"
print main.__doc__
sys.exit()
vol = 10.5e-6 # default for spinner program
if "-V" in args:
ind = args.index("-V")
vol = float(args[ind + 1]) * 1e-6 # convert volume to m^3
if "-A" in args: noave = 1
if '-LP' in args:
ind = args.index("-LP")
codelist = args[ind + 1]
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
methcode = "LT-AF-Z"
if "T" in codes:
demag = "T"
methcode = "LT-T-Z"
if "I" in codes:
methcode = "LP-IRM"
if "A" in codes:
methcode = "LT-AF-I"
dc = '%10.3e' % (1e-3 * float(args[ind + 1]))
MagRecs = []
version_num = pmag.get_version()
meas_file = dir_path + '/' + meas_file
for line in input.readlines():
instcode = "ODP-MSPN"
rec = line.split()
if len(rec) > 2 and "Leg" not in line:
MagRec = {}
MagRec['er_expedition_name'] = rec[0]
MagRec['er_location_name'] = rec[1] + rec[2]
MagRec["er_specimen_name"] = rec[0] + '-' + 'U' + rec[1] + rec[
2].upper() + "-" + rec[3] + rec[4].upper(
) + '-' + rec[5] + '-' + 'W' + '-' + rec[6]
MagRec["er_site_name"] = MagRec['er_specimen_name']
MagRec["er_sample_name"] = MagRec['er_specimen_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"] = dc
MagRec["treatment_dc_field_phi"] = '0'
MagRec["treatment_dc_field_theta"] = '0'
meas_type = "LT-NO"
if float(rec[11]) == 0:
pass
elif demag == "AF":
MagRec["treatment_ac_field"] = '%8.3e' % (
float(rec[11]) * 1e-3) # peak field in tesla
meas_type = "LT-AF-Z"
MagRec["treatment_dc_field"] = '0'
else:
MagRec["treatment_temp"] = '%8.3e' % (float(rec[11]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
intens = 1e-3 * float(rec[10]) * vol # convert mA/m to Am^2
MagRec["measurement_magn_moment"] = '%10.3e' % (intens)
MagRec["measurement_dec"] = rec[8]
MagRec["measurement_inc"] = rec[9]
MagRec["magic_instrument_codes"] = "ODP-MSPN"
MagRec["er_analyst_mail_names"] = user
MagRec["er_citation_names"] = citation
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_flag"] = 'g'
MagRec["measurement_csd"] = ''
MagRec["measurement_number"] = '1'
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print "results put in ", meas_file
def main(command_line=True, **kwargs):
"""
NAME
iodp_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
iodp_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'r')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'r')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave = 0
volume = 2.5**3 #default volume is a 2.5cm cube
inst = ""
samp_con, Z = '5', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
dir_path = '.'
MagRecs = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
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]
if samp_file[0] != '/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file, 'r')
ErSamps, file_type = pmag.magic_read(samp_file)
except:
print(samp_file, ' not found: ')
print(
' download csv file and import to MagIC with iodp_samples_magic.py'
)
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args:
noave = 1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print("You must provide an IODP_jr6 format file")
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print(
'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'
.format(mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(
mag_file)
if not os.path.exists(samp_file):
print(
"Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one"
.format(input_dir_path))
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(
input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
samples, filetype = pmag.magic_read(samp_file)
with open(temp, 'r') as finput:
lines = finput.readlines()
os.remove(temp)
for line in lines:
MagRec = {}
line = line.split()
spec_text_id = line[0].split('_')[1]
SampRecs = pmag.get_dictitem(samples, 'er_sample_alternatives',
spec_text_id, 'has')
if len(SampRecs) > 0: # found one
MagRec['er_specimen_name'] = SampRecs[0]['er_sample_name']
MagRec['er_sample_name'] = MagRec['er_specimen_name']
MagRec['er_site_name'] = MagRec['er_specimen_name']
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["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["treatment_ac_field"] = '0'
volume = float(SampRecs[0]['sample_volume'])
x = float(line[4])
y = float(line[3])
negz = float(line[2])
cart = np.array([x, y, -negz]).transpose()
direction = pmag.cart2dir(cart).transpose()
expon = float(line[5])
magn_volume = direction[2] * (10.0**expon)
moment = magn_volume * volume
MagRec["measurement_magn_moment"] = str(moment)
MagRec["measurement_magn_volume"] = str(
magn_volume) #str(direction[2] * (10.0 ** expon))
MagRec["measurement_dec"] = '%7.1f' % (direction[0])
MagRec["measurement_inc"] = '%7.1f' % (direction[1])
step = line[1]
if step == 'NRM':
meas_type = "LT-NO"
elif step[0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(step[2:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif step[0:2] == 'TD':
meas_type = "LT-T-Z"
treat = float(step[2:])
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
elif step[0:3] == 'ARM': #
meas_type = "LT-AF-I"
treat = float(row['step'][3:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"] = '%8.3e' % (
50e-6) # assume 50uT DC field
MagRec[
"measurement_description"] = 'Assumed DC field - actual unknown'
elif step[0:3] == 'IRM': #
meas_type = "LT-IRM"
treat = float(step[3:])
MagRec["treatment_dc_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
else:
print('unknown treatment type for ', row)
return False, 'unknown treatment type for ', row
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec.copy())
else:
print('sample name not found: ', row['specname'])
MagOuts = pmag.measurements_methods(MagRecs, noave)
file_created, error_message = pmag.magic_write(meas_file, MagOuts,
'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main():
"""
NAME
odp_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
odp_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-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
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
else:
samp_file=dir_path+'/'+samp_file
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=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 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
spec_file=dir_path+'/'+spec_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower()=='dsc':
print('processing: ',file)
MagRec,SpecRec,SampRec={},{},{}
treatment_type,treatment_value,user="","",""
inst="ODP-SRM"
input=open(dir_path+'/'+file,'r').readlines()
IDs=file.split('_') # splits on underscores
pieces=IDs[0].split('-')
expedition=pieces[0]
location=pieces[1]
if file[0]!='_':
while len(pieces[2])<4:pieces[2]='0'+pieces[2] # pad core to be 3 characters
specimen=""
else:
specimen="test"
for piece in pieces:
specimen=specimen+piece+'-'
specimen=specimen[:-1]
alt_spec=IDs[1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_sample_name']=specimen
SpecRec['er_citation_names']=citation
for key in list(SpecRec.keys()):SampRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
SpecRec['er_specimen_name']=specimen
SampRec['er_specimen_names']=specimen
for key in list(SpecRec.keys()):MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
for k in range(len(input)):
fields= input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst=inst+':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type="IRM"
if "treatment_value" in fields[0]:
values=fields[1].split(',')
value=values[0]
if value!=" \n":
if treatment_type=="AF":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif treatment_type=="IRM":
treatment_value=float(value)*1e-3
MagRec["treatment_dc_field"]='%8.3e'%(treatment_value) # IRM treat mT => T
if treatment_type=="ARM":
treatment_value=float(value)*1e-3
dc_value=float(values[1])*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"]='%8.3e'%(dc_value) # DC mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"]=fields[-1]
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
if input[k][0:7]=='<MULTI>':
rec=input[k+1].split(',') # list of data
for item in rec:
items=item.split('=')
if items[0].strip()=='demag_level' and treatment_value=="" :
treat= float(items[1])
if treat!=0:
MagRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MagRec["treatment_ac_field"]=treat*1e-3 # AF demag in treat mT => T
if items[0].strip()=='inclination_w_tray_w_bkgrd': MagRec['measurement_inc']=items[1]
if items[0].strip()=='declination_w_tray_w_bkgrd': MagRec['measurement_dec']=items[1]
if items[0].strip()=='intensity_w_tray_w_bkgrd': MagRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
if items[0].strip()=='x_stdev':MagRec['measurement_x_sd']=items[1]
if items[0].strip()=='y_stdev':MagRec['measurement_y_sd']=items[1]
if items[0].strip()=='z_stdev':MagRec['measurement_sd_z']=items[1]
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts=pmag.sort_diclist(MagRecs,'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec["treatment_ac_field"]) # convert to string
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print('samples stored in ',samp_file)
pmag.magic_write(samp_file,SampRecs,'er_samples')
print('specimens stored in ',spec_file)
Fixed=pmag.measurements_methods(MagOuts,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print('data stored in ',meas_file)
def main(command_line=True, **kwargs):
"""
NAME
jr6_txt_magic.py
DESCRIPTION
converts JR6 .txt format files to magic_measurements format files
SYNTAX
jr6_txt_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume of the sample, default 2.5cm^3.
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.
INPUT
JR6 .txt format file
"""
# initialize some stuff
noave=0
volume = 2.5 * 1e-6 # default volume is 2.5 cm^3 (2.5 * 1e-6 meters^3)
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
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]
#try:
# open(samp_file,'r')
# 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 = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if "-v" in args:
ind=args.index("-v")
volume=float(args[ind+1]) * 1e-6
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
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")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
ErSampRec,ErSiteRec={},{}
# parse data
data=open(mag_file,'r')
line=data.readline()
line=data.readline()
line=data.readline()
while line !='':
parsedLine=line.split()
sampleName=parsedLine[0]
demagLevel=parsedLine[2]
date=parsedLine[3]
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
parsedLine=line.split()
specimenAngleDec=parsedLine[1]
specimenAngleInc=parsedLine[2]
while parsedLine[0] != 'MEAN' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
Mx=parsedLine[1]
My=parsedLine[2]
Mz=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
splitExp = parsedLine[2].split('A')
intensityVolStr=parsedLine[1] + splitExp[0]
intensityVol = float(intensityVolStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr=''
if len(parsedLine) == 6: #normal line
precisionStr=parsedLine[5][0:-1]
else:
precisionStr=parsedLine[4][0:-1]
precisionPer = float(precisionStr)
precision=intensityVol*precisionPer/100
while parsedLine[0] != 'SPEC.' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
specimenDec=parsedLine[2]
specimenInc=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
geographicDec=parsedLine[1]
geographicInc=parsedLine[2]
# Add data to various MagIC data tables.
er_specimen_name = sampleName
if specnum!=0:
er_sample_name=er_specimen_name[:specnum]
else:
er_sample_name=er_specimen_name
if int(samp_con) in [1, 2, 3, 4, 5, 7]:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
else:
print("-W- Using unreognized sample convention option: ", samp_con)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# check sample list(SampOuts) to see if sample already exists in list before adding new sample info
sampleFlag=0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == er_sample_name:
sampleFlag=1
break
if sampleFlag == 0:
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['sample_azimuth']=specimenAngleDec
sample_dip=str(float(specimenAngleInc)-90.0) #convert to magic orientation
ErSampRec['sample_dip']=sample_dip
ErSampRec['magic_method_codes']=meth_code
ErSampRec['er_location_name']=er_location_name
ErSampRec['er_site_name']=er_site_name
ErSampRec['er_citation_names']='This study'
SampOuts.append(ErSampRec.copy())
MagRec={}
MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_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["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
MagRec["treatment_ac_field"]='0'
if demagLevel == 'NRM':
meas_type="LT-NO"
elif demagLevel[0] == 'A':
meas_type="LT-AF-Z"
treat=float(demagLevel[1:])
MagRec["treatment_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:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown", demag_level)
return False, "measurement type unknown"
MagRec["measurement_magn_moment"]=str(intensityVol*volume) # Am^2
MagRec["measurement_magn_volume"]=intensityVolStr # A/m
MagRec["measurement_dec"]=specimenDec
MagRec["measurement_inc"]=specimenInc
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
#read lines till end of record
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
# read all the rest of the special characters. Some data files not consistantly formatted.
while (len(line) <=3 and line!=''):
line=data.readline()
#end of data while loop
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(samp_file,SampOuts,'er_samples')
print("sample orientations put in ",samp_file)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print("results put in ",meas_file)
return True, meas_file
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(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-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
-dm: specify which magic data model you want your output in 3.0 or 2.5 default is 2.5
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
NOTES:
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 = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
"""
#
#initialize variables
norm='cc'
samp_con,Z='3',1
meas_file='measurements.txt'
spec_file='specimens.txt'
samp_file='samples.txt'
site_file='sites.txt'
Specs,Samps,Sites,Locs=[],[],[],[]
MeasRecs=[]
specnum,units,locname=0,"1","unknown"
citation="This study"
dir_path='.'
args=sys.argv
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
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 '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-Fsi' in args: # LORI addition
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-loc' in args:
ind=args.index("-loc")
locname=args[ind+1]
if '-mcd' in args:
ind=args.index("-mcd")
methods=args[ind+1]
else:
methods='SO-MAG'
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if '-n' in args:
ind=args.index("-n")
norm=args[ind+1]
if "-A" in args:
avg=1
else:
avg=0
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")
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 '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if '-dm' in args:
dmi = args.index('-dm')
data_model = args[dmi+1]
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('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
data_model = kwargs.get('data_model', 2.5) # data_model to output as
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
# done with module-specific stuff
# formatting and checking variables
if "4" in samp_con:
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"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file= os.path.join(output_dir_path, meas_file)
try:
file_input=open(magfile,'r')
except Exception as ex:
print("bad sam file name: ", magfile)
return False, "bad sam file name"
File = file_input.readlines()
if len(File) == 1: File = File[0].split('\r'); File = [x+"\r\n" for x in File]
sids,ln,format=[],0,'CIT'
formats=['CIT','2G','APP','JRA']
if File[ln].strip()=='CIT': ln+=1
LocRec={}
LocRec["er_location_name"]=locname
LocRec["er_citation_names"]=citation
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print(comment)
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
LocRec["location_begin_lat"]=site_lat
LocRec["location_begin_lon"]=site_lon
LocRec["location_end_lat"]=site_lat
LocRec["location_end_lon"]=site_lon
Locs.append(LocRec)
try: Cdec=float(line[2])
except ValueError: pdb.set_trace()
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
if rec == []: continue
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
SpecRec,SampRec,SiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
SpecRec['er_specimen_name']=specimen
SpecRec['er_sample_name']=sample
SpecRec['er_site_name']=site
SpecRec['er_location_name']=locname
SpecRec['er_citation_names']=citation
SampRec['er_sample_name']=sample
SampRec['er_site_name']=site
SampRec['er_location_name']=locname
SampRec['er_citation_names']=citation
SampRec['magic_method_codes']=methods
SampRec['sample_declination_correction']='%7.1f'%(Cdec)
SiteRec['er_site_name']=site
SiteRec['er_location_name']=locname
SiteRec['er_citation_names']=citation
SiteRec['site_lat']=site_lat
SiteRec['site_lon']=site_lon
f=open(input_dir_path+'/'+specimen,'rU')
Lines=f.readlines()
comment=""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
vol=float(info[-1])
if vol!=1.0:
if norm=='cc':units="1"
if norm=='m3':units="2"
SpecRec['specimen_weight']=""
if units=="1" or "":
SpecRec['specimen_volume']='%10.3e'%(vol*1e-6)
else:
SpecRec['specimen_volume']='%10.3e'%(vol)
else:
if norm=='cc':units="1"
if norm=='m3':units="2"
SpecRec['specimen_volume']=""
if units=="1" or "":
SpecRec['specimen_weight']='%10.3e'%(vol*1e-3)
else:
SpecRec['specimen_weight']='%10.3e'%(vol)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
SampRec['sample_height']=info[-6]
else:
SampRec['sample_height']='0'
SampRec['sample_azimuth']='%7.1f'%(sample_azimuth)
SampRec['sample_dip']='%7.1f'%(sample_dip)
SampRec['sample_bed_dip']='%7.1f'%(dip)
SampRec['sample_bed_dip_direction']='%7.1f'%(dip_direction)
SampRec['sample_class']=''
SampRec['sample_type']=''
SampRec['sample_lithology']=''
if Cdec!=0 or Cdec!="":
SampRec['magic_method_codes']='SO-CMD-NORTH'
else:
SampRec['magic_method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
#print 'line:', line
MeasRec=SpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type=line[0:3]
treat=line[2:6]
try: float(treat)
except ValueError: treat = line[3:6]
if treat_type.startswith('NRM'):
MeasRec['magic_method_codes']='LT-NO'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
elif treat_type.startswith('AF'):
MeasRec['magic_method_codes']='LT-AF-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
if treat.strip() == '':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('ARM'):
MeasRec['magic_method_codes']="LP-ARM"
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
if treat.strip() == '':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['magic_method_codes']="LP-ARM-AFD"
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('TT'):
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['measurement_temp']='273'
if treat.strip() == '':
MeasRec['treatment_temp']='273'
else:
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
elif treat_type.startswith('LT') or treat_type.startswith('LN2'):
MeasRec['magic_method_codes']='LT-LT-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='77'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
else:
print("trouble with your treatment steps")
MeasRec['measurement_dec']=line[46:51]
MeasRec['measurement_inc']=line[52:58]
M='%8.2e'%(float(line[31:39])*vol*1e-3) # convert to Am2
MeasRec['measurement_magn_moment']=M
MeasRec['measurement_csd']='%7.1f'%(eval(line[41:46]))
MeasRec["measurement_positions"]='1'
MeasRec['measurement_standard']='u'
if len(line)>60:
MeasRec['magic_instrument_codes']=line[85:].strip('\n \r \t "')
MeasRec['measurement_sd_x']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['measurement_sd_z']='%8.2e'%(float(line[76:85])*1e-8)
MeasRecs.append(MeasRec)
Specs.append(SpecRec)
if sample not in samples:
samples.append(sample)
Samps.append(SampRec)
site=pmag.parse_site(sample,samp_con,Z)
if site not in sites:
sites.append(site)
Sites.append(SiteRec)
if float(data_model)==3.0:
con = nb.Contribution('.',read_tables=[])
con.add_empty_magic_table('specimens')
con.add_empty_magic_table('samples')
con.add_empty_magic_table('sites')
con.add_empty_magic_table('locations')
con.add_empty_magic_table('measurements')
con.tables['specimens'].df = DataFrame(Specs).rename(columns=mapm.spec_magic2_2_magic3_map)
con.tables['samples'].df = DataFrame(Samps).rename(columns=mapm.samp_magic2_2_magic3_map)
con.tables['sites'].df = DataFrame(Sites).rename(columns=mapm.site_magic2_2_magic3_map)
con.tables['locations'].df = DataFrame(Locs).rename(columns=mapm.loc_magic2_2_magic3_map)
Fixed=pmag.measurements_methods(MeasRecs,avg)
con.tables['measurements'].df = DataFrame(Fixed).rename(columns=mapm.meas_magic2_2_magic3_map)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
print('specimens stored in ',spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
print('samples stored in ',samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
print('sites stored in ', site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
print('locations stored in ', loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
print('data stored in ',meas_file)
else:
pmag.magic_write(spec_file,Specs,'er_specimens')
print('specimens stored in ',spec_file)
pmag.magic_write(samp_file,Samps,'er_samples')
print('samples stored in ',samp_file)
pmag.magic_write(site_file,Sites,'er_sites')
print('sites stored in ', site_file)
Fixed=pmag.measurements_methods(MeasRecs,avg)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print('data stored in ',meas_file)
return True, meas_file
return True, meas_file
def main():
"""
NAME
odp_srm_magic.py
DESCRIPTION
converts ODP measurement format files to magic_measurements format files
SYNTAX
odp_srm_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsa FILE: specify output er_sample.txt file, default is er_sample.txt
-A : don't average replicate measurements
INPUT
put data from a single core into a directory. depths will be below core top
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
samp_file='er_samples.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0,
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
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]
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
samp_file=dir_path+'/'+samp_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for file in filelist: # parse each file
if file[-3:].lower()=='srm':
print 'processing: ',file
Nfo=file.split('_')[0].split('-')
try:
sect=int(Nfo[3][:-1])
except:
sect=1
input=open(file,'rU').readlines()
MagRec,SpecRec,SampRec={},{},{}
alt_spec,treatment_type,treatment_value,user="","","",""
inst="ODP-SRM"
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_code']='FS-C-DRILL-IODP:SP-SS-C'
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
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'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
treatment_value,inst="","ODP-SRM"
k=0
while 1:
fields= input[k].replace('\n','').split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
if "treatment_value" in fields[0]:
value=fields[1]
if value!=" ":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]='%8.3e'%(treatment_value) # AF demag in treat mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
k+=1
if input[k][0:7]=='<MULTI>':
break
while 1:
k+=1
line = input[k]
if line[0:5]=='<RAW>':
break
treatment_value=""
rec=line.replace('\n','').split(',') # list of data
if len(rec)>2:
MeasRec,SampRec={},{'core_depth':'0','er_sample_name':'0','er_site_name':'0','er_location_name':'location'}
for key in MagRec.keys():MeasRec[key]=MagRec[key]
for item in rec:
items=item.split('=')
if 'demag_level' in items[0]:
treat= float(items[1])
if treat!=0:
MeasRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MeasRec["treatment_ac_field"]='%8.3e'%(treat*1e-3) # AF demag in treat mT => T
if 'inclination_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_inc']=items[1]
if 'declination_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_dec']=items[1]
if 'intensity_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
MeasRec['magic_instrument_codes']=inst
if 'offset' in items[0]:
depth='%7.3f'%(float(sect-1)*1.5+float(items[1]))
SampRec['core_depth']=depth
MeasRec['er_specimen_name']=depth
MeasRec['er_sample_name']=depth
MeasRec['er_site_name']=depth
MeasRec['er_location_name']='location'
SampRec['er_sample_name']=depth
SampRec['er_site_name']=depth
SampRec['er_location_name']='location'
MeasRec['measurement_number']='1'
SampRecs.append(SampRec)
MagRecs.append(MeasRec)
pmag.magic_write(samp_file,SampRecs,'er_samples')
print 'samples stored in ',samp_file
Fixed=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file