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():
"""
NAME
huji_sample_magic.py
DESCRIPTION
takes tab delimited Hebrew University sample file and converts to MagIC formatted tables
SYNTAX
huji_sample_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify sample output file, default is: er_samples.txt
-Fsi FILE: specify site output file, default is: er_sites.txt
-Iso: import sample orientation info - default is to set sample_az/dip to 0,0
-ncn NCON: specify naming convention: default is #1 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
-loc: location name, default="unknown"
INPUT FORMAT
Input files must be tab delimited:
Samp Az Dip Dip_dir Dip
Orientation convention:
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
e.g. field_dip is degrees from horizontal of drill direction
Magnetic declination convention:
Az is already corrected in file
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 er_samples.txt will overwrite any existing files
"""
#
# initialize variables
#
version_num = pmag.get_version()
samp_file, or_con, corr = "er_samples.txt", "1", "1"
site_file = 'er_sites.txt'
args = sys.argv
date, lat, lon = "", "", "" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip, bed_dip_dir = "", ""
participantlist = ""
sites = [] # list of site names
Lats, Lons = [], [] # list of latitudes and longitudes
SampRecs, SiteRecs, ImageRecs, imagelist = [], [], [], [
] # lists of Sample records and Site records
samp_con, Z, average_bedding = "1", 1, "0"
newbaseline, newbeddir, newbeddip = "", "", ""
meths = 'FS-FD:SO-POM:SO-SUN'
delta_u = "0"
sclass, lithology, type = "", "", ""
newclass, newlith, newtype = '', '', ''
user = ""
or_con = '3'
corr == "3"
DecCorr = 0.
location_name = "unknown"
ignore = 1
#
#
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-f" in args:
ind = args.index("-f")
orient_file = sys.argv[ind + 1]
else:
"Must have orientation file name"
sys.exit()
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = sys.argv[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 3-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
print(samp_con, Z)
if "-mcd" in args:
ind = args.index("-mcd")
meths = (sys.argv[ind + 1])
if "-loc" in args:
ind = args.index("-loc")
location_name = (sys.argv[ind + 1])
if "-Iso" in args: ignore = 0
#
# read in file to convert
#
azfile = open(orient_file, 'r')
AzDipDat = azfile.readlines()
azfile.close()
SampOut = []
SiteOut = []
for line in AzDipDat[1:]:
orec = line.split()
if len(orec) > 1:
labaz, labdip = pmag.orient(float(orec[1]), float(orec[2]), or_con)
bed_dip_dir = (orec[3])
bed_dip = (orec[4])
SampRec = {}
SiteRec = {}
SampRec["er_location_name"] = location_name
SampRec["er_citation_names"] = "This study"
SiteRec["er_location_name"] = location_name
SiteRec["er_citation_names"] = "This study"
SiteRec["site_class"] = ""
SiteRec["site_lithology"] = ""
SiteRec["site_type"] = ""
SiteRec["site_definition"] = "s"
SiteRec["er_citation_names"] = "This study"
#
# parse information common to all orientation methods
#
SampRec["er_sample_name"] = orec[0]
SampRec["sample_bed_dip_direction"] = orec[3]
SampRec["sample_bed_dip"] = orec[4]
SiteRec["site_bed_dip_direction"] = orec[3]
SiteRec["site_bed_dip"] = orec[4]
if ignore == 0:
SampRec["sample_dip"] = '%7.1f' % (labdip)
SampRec["sample_azimuth"] = '%7.1f' % (labaz)
else:
SampRec["sample_dip"] = '0'
SampRec["sample_azimuth"] = '0'
SampRec["sample_lat"] = orec[5]
SampRec["sample_lon"] = orec[6]
SiteRec["site_lat"] = orec[5]
SiteRec["site_lon"] = orec[6]
methods = meths.split(":")
SampRec["magic_method_codes"] = meths
site = pmag.parse_site(orec[0], samp_con,
Z) # parse out the site name
SampRec["er_site_name"] = site
SampRec['magic_software_packages'] = version_num
SiteRec["er_site_name"] = site
SiteRec['magic_software_packages'] = version_num
SampOut.append(SampRec)
SiteOut.append(SiteRec)
pmag.magic_write(samp_file, SampOut, "er_samples")
print("Sample info saved in ", samp_file)
pmag.magic_write(site_file, SiteOut, "er_sites")
print("Site info saved in ", site_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 convert(**kwargs):
#
# initialize variables
#
bed_dip,bed_dip_dir="",""
sclass,lithology,_type="","",""
DecCorr=0.
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', 'FS-FD:SO-POM')
location = kwargs.get('location', 'unknown')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
user = kwargs.get('user', '')
noave = kwargs.get('noave', 0) # default is DO average
ID = kwargs.get('ID', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
# format and fix variables acquired from command line sys.argv or input with **kwargs
if specnum!=0:specnum=-specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
Z = 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, "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:
print('Naming convention option [6] not currently supported')
return False, 'Naming convention option [6] not currently supported'
#Z=1
#try:
# SampRecs,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"
#else: Z=1
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)
samplist=[]
try:
SampRecs,file_type=pmag.magic_read(samp_file)
except:
SampRecs=[]
MeasRecs,SpecRecs,SiteRecs,LocRecs=[],[],[],[]
try:
f=open(mag_file,'br')
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
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths = reduce(lambda x,y: x+':'+y, methods)
method_codes=meths
site=pmag.parse_site(sample,samp_con,Z) # parse out the site name
SpecRec,SampRec,SiteRec,LocRec={},{},{},{}
SpecRec["specimen"]=specname
SpecRec["sample"]=sample
if vcc.strip()!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SpecRec["volumne"]='%10.3e'%(vol) #
SpecRec["geologic_classes"]=sclass
SpecRec["lithologies"]=lithology
SpecRec["geologic_types"]=_type
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec["sample"]=sample
SampRec["site"]=site
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
SampRec["bed_dip"]='%7.1f'%(bed_dip)
SampRec["bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["dip"]='%7.1f'%(labdip)
SampRec["azimuth"]='%7.1f'%(labaz)
SampRec["azimuth_dec_correction"]='%7.1f'%(deccorr)
SampRec["geologic_classes"]=sclass
SampRec["lithologies"]=lithology
SampRec["geologic_types"]=_type
SampRec["method_codes"]=method_codes
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec["geologic_classes"]=sclass
SiteRec["lithologies"]=lithology
SiteRec["geologic_types"]=_type
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRec["geologic_classes"]=sclass
LocRec["lithologies"]=lithology
LocRec["geologic_types"]=_type
LocRecs.append(LocRec)
else:
MeasRec={}
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
meas_type="LT-NO"
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["specimen"]=specname
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MeasRec["dir_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MeasRec["dir_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]
MeasRec["magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MeasRec["magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MeasRec["magn_x_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MeasRec["magn_y_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MeasRec["magn_z_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MeasRec["meas_n_orient"]=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]
# MeasRec['measurement_date']=dstring
MeasRec["instrument_codes"]=inst
MeasRec["analysts"]=user
MeasRec["citations"]="This study"
MeasRec["method_codes"]=meas_type
if demag=="AF":
MeasRec["treat_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MeasRec["treat_dc_field"]='0'
elif demag=="T":
MeasRec["treat_temp"]='%8.3e' % (float(treat[:-1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
con.write_table_to_file('measurements', custom_name=meas_file)
return True, meas_file
def main():
"""
NAME
huji_sample_magic.py
DESCRIPTION
takes tab delimited Hebrew University sample file and converts to MagIC formatted tables
SYNTAX
huji_sample_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify sample output file, default is: er_samples.txt
-Fsi FILE: specify site output file, default is: er_sites.txt
-Iso: import sample orientation info - default is to set sample_az/dip to 0,0
-ncn NCON: specify naming convention: default is #1 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
-loc: location name, default="unknown"
INPUT FORMAT
Input files must be tab delimited:
Samp Az Dip Dip_dir Dip
Orientation convention:
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
e.g. field_dip is degrees from horizontal of drill direction
Magnetic declination convention:
Az is already corrected in file
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 er_samples.txt will overwrite any existing files
"""
#
# initialize variables
#
version_num=pmag.get_version()
samp_file,or_con,corr = "er_samples.txt","1","1"
site_file='er_sites.txt'
args=sys.argv
date,lat,lon="","","" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip,bed_dip_dir="",""
participantlist=""
sites=[] # list of site names
Lats,Lons=[],[] # list of latitudes and longitudes
SampRecs,SiteRecs,ImageRecs,imagelist=[],[],[],[] # lists of Sample records and Site records
samp_con,Z,average_bedding="1",1,"0"
newbaseline,newbeddir,newbeddip="","",""
meths='FS-FD:SO-POM:SO-SUN'
delta_u="0"
sclass,lithology,type="","",""
newclass,newlith,newtype='','',''
user=""
or_con='3'
corr=="3"
DecCorr=0.
location_name="unknown"
ignore=1
#
#
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-f" in args:
ind=args.index("-f")
orient_file=sys.argv[ind+1]
else:
"Must have orientation file name"
sys.exit()
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 3-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
print(samp_con, Z)
if "-mcd" in args:
ind=args.index("-mcd")
meths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-Iso" in args: ignore=0
#
# read in file to convert
#
azfile=open(orient_file,'r')
AzDipDat=azfile.readlines()
azfile.close()
SampOut=[]
SiteOut=[]
for line in AzDipDat[1:]:
orec=line.split()
if len(orec)>1:
labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)
bed_dip_dir=(orec[3])
bed_dip=(orec[4])
SampRec={}
SiteRec={}
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
SiteRec["er_location_name"]=location_name
SiteRec["er_citation_names"]="This study"
SiteRec["site_class"]=""
SiteRec["site_lithology"]=""
SiteRec["site_type"]=""
SiteRec["site_definition"]="s"
SiteRec["er_citation_names"]="This study"
#
# parse information common to all orientation methods
#
SampRec["er_sample_name"]=orec[0]
SampRec["sample_bed_dip_direction"]=orec[3]
SampRec["sample_bed_dip"]=orec[4]
SiteRec["site_bed_dip_direction"]=orec[3]
SiteRec["site_bed_dip"]=orec[4]
if ignore==0:
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
else:
SampRec["sample_dip"]='0'
SampRec["sample_azimuth"]='0'
SampRec["sample_lat"]=orec[5]
SampRec["sample_lon"]=orec[6]
SiteRec["site_lat"]=orec[5]
SiteRec["site_lon"]=orec[6]
methods=meths.split(":")
SampRec["magic_method_codes"]=meths
site=pmag.parse_site(orec[0],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
SampRec['magic_software_packages']=version_num
SiteRec["er_site_name"]=site
SiteRec['magic_software_packages']=version_num
SampOut.append(SampRec)
SiteOut.append(SiteRec)
pmag.magic_write(samp_file,SampOut,"er_samples")
print("Sample info saved in ", samp_file)
pmag.magic_write(site_file,SiteOut,"er_sites")
print("Site info saved in ", site_file)
def convert(**kwargs):
#
# initialize variables
#
bed_dip, bed_dip_dir = "", ""
sclass, lithology, _type = "", "", ""
DecCorr = 0.
months = [
'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct',
'Nov', 'Dec'
]
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', 'FS-FD:SO-POM')
location = kwargs.get('location', 'unknown')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
user = kwargs.get('user', '')
noave = kwargs.get('noave', 0) # default is DO average
ID = kwargs.get('ID', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
# format and fix variables acquired from command line sys.argv or input with **kwargs
if specnum != 0: specnum = -specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
Z = 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, "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:
print('Naming convention option [6] not currently supported')
return False, 'Naming convention option [6] not currently supported'
#Z=1
#try:
# SampRecs,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"
#else: Z=1
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)
samplist = []
try:
SampRecs, file_type = pmag.magic_read(samp_file)
except:
SampRecs = []
MeasRecs, SpecRecs, SiteRecs, LocRecs = [], [], [], []
try:
f = open(mag_file, 'br')
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
methods = gmeths.split(':')
if deccorr != "0":
if 'SO-MAG' in methods: del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths = reduce(lambda x, y: x + ':' + y, methods)
method_codes = meths
site = pmag.parse_site(sample, samp_con,
Z) # parse out the site name
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}
SpecRec["specimen"] = specname
SpecRec["sample"] = sample
if vcc.strip() != "":
vol = float(vcc) * 1e-6 # convert to m^3 from cc
SpecRec["volumne"] = '%10.3e' % (vol) #
SpecRec["geologic_classes"] = sclass
SpecRec["lithologies"] = lithology
SpecRec["geologic_types"] = _type
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec["sample"] = sample
SampRec["site"] = site
labaz, labdip = pmag.orient(az, pl,
or_con) # convert to labaz, labpl
SampRec["bed_dip"] = '%7.1f' % (bed_dip)
SampRec["bed_dip_direction"] = '%7.1f' % (bed_dip_dir)
SampRec["dip"] = '%7.1f' % (labdip)
SampRec["azimuth"] = '%7.1f' % (labaz)
SampRec["azimuth_dec_correction"] = '%7.1f' % (deccorr)
SampRec["geologic_classes"] = sclass
SampRec["lithologies"] = lithology
SampRec["geologic_types"] = _type
SampRec["method_codes"] = method_codes
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else ""
for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec["geologic_classes"] = sclass
SiteRec["lithologies"] = lithology
SiteRec["geologic_types"] = _type
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRec["geologic_classes"] = sclass
LocRec["lithologies"] = lithology
LocRec["geologic_types"] = _type
LocRecs.append(LocRec)
else:
MeasRec = {}
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
meas_type = "LT-NO"
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["specimen"] = specname
el, demag = 1, ''
treat = rec[el]
if treat[-1] == 'C':
demag = 'T'
elif treat != 'NRM':
demag = 'AF'
el += 1
while rec[el] == "":
el += 1
MeasRec["dir_dec"] = rec[el]
cdec = float(rec[el])
el += 1
while rec[el] == "":
el += 1
MeasRec["dir_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]
MeasRec["magn_moment"] = '%10.3e' % (float(rec[el]) * 1e-3
) # moment in Am^2 (from emu)
MeasRec["magn_volume"] = '%10.3e' % (float(rec[el]) * 1e-3 / vol
) # magnetization in A/m
el = skip(2, el, rec) # skip to xsig
MeasRec["magn_x_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to ysig
MeasRec["magn_y_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to zsig
MeasRec["magn_z_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el += 1 # skip to positions
MeasRec["meas_n_orient"] = 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]
# MeasRec['measurement_date']=dstring
MeasRec["instrument_codes"] = inst
MeasRec["analysts"] = user
MeasRec["citations"] = "This study"
MeasRec["method_codes"] = meas_type
if demag == "AF":
MeasRec["treat_ac_field"] = '%8.3e' % (float(treat[:-2]) * 1e-3
) # peak field in tesla
meas_type = "LT-AF-Z"
MeasRec["treat_dc_field"] = '0'
elif demag == "T":
MeasRec["treat_temp"] = '%8.3e' % (float(treat[:-1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
con.write_table_to_file('measurements', custom_name=meas_file)
return True, meas_file
