def main():
"""
NAME
di_geo.py
DESCRIPTION
rotates specimen coordinate dec, inc data to geographic
coordinates using the azimuth and plunge of the X direction
INPUT FORMAT
declination inclination azimuth plunge
SYNTAX
di_geo.py [-h][-i][-f FILE] [< filename ]
OPTIONS
-h prints help message and quits
-i for interactive data entry
-f FILE command line entry of file name
-F OFILE, specify output file, default is standard output
OUTPUT:
declination inclination
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-F' in sys.argv:
ind = sys.argv.index('-F')
ofile = sys.argv[ind + 1]
out = open(ofile, 'w')
print ofile, ' opened for output'
else:
ofile = ""
if '-i' in sys.argv: # interactive flag
while 1:
try:
Dec = float(raw_input("Declination: <cntrl-D> to quit "))
except EOFError:
print "\n Good-bye\n"
sys.exit()
Inc = float(raw_input("Inclination: "))
Az = float(raw_input("Azimuth: "))
Pl = float(raw_input("Plunge: "))
print '%7.1f %7.1f' % (pmag.dogeo(Dec, Inc, Az, Pl))
elif '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
data = numpy.loadtxt(file)
else:
data = numpy.loadtxt(
sys.stdin, dtype=numpy.float) # read in the data from the datafile
D, I = pmag.dogeo_V(data)
for k in range(len(D)):
if ofile == "":
print '%7.1f %7.1f' % (D[k], I[k])
else:
out.write('%7.1f %7.1f\n' % (D[k], I[k]))
def main():
"""
NAME
di_geo.py
DESCRIPTION
rotates specimen coordinate dec, inc data to geographic
coordinates using the azimuth and plunge of the X direction
INPUT FORMAT
declination inclination azimuth plunge
SYNTAX
di_geo.py [-h][-i][-f FILE] [< filename ]
OPTIONS
-h prints help message and quits
-i for interactive data entry
-f FILE command line entry of file name
-F OFILE, specify output file, default is standard output
OUTPUT:
declination inclination
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
ofile=sys.argv[ind+1]
out=open(ofile,'w')
print ofile, ' opened for output'
else: ofile=""
if '-i' in sys.argv: # interactive flag
while 1:
try:
Dec=float(raw_input("Declination: <cntrl-D> to quit "))
except EOFError:
print "\n Good-bye\n"
sys.exit()
Inc=float(raw_input("Inclination: "))
Az=float(raw_input("Azimuth: "))
Pl=float(raw_input("Plunge: "))
print '%7.1f %7.1f'%(pmag.dogeo(Dec,Inc,Az,Pl))
elif '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
data=numpy.loadtxt(file)
else:
data=numpy.loadtxt(sys.stdin,dtype=numpy.float) # read in the data from the datafile
D,I=pmag.dogeo_V(data)
for k in range(len(D)):
if ofile=="":
print '%7.1f %7.1f'%(D[k],I[k])
else:
out.write('%7.1f %7.1f\n'%(D[k],I[k]))
def main():
"""
NAME
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimens.txt file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
allows testing and reject specimens for bad orientations
SYNTAX
site_edit_magic.py [command line options]
OPTIONS
-h: prints help and quits
-f: specify pmag_specimen format file, default is pmag_specimens.txt
-fsa: specify er_samples.txt file
-exc: use existing pmag_criteria.txt file
-N: reset all sample flags to good
OUPUT
edited er_samples.txt file
"""
dir_path='.'
FIG={} # plot dictionary
FIG['eqarea']=1 # eqarea is figure 1
in_file='pmag_specimens.txt'
sampfile='er_samples.txt'
out_file=""
fmt,plot='svg',1
Crits=""
M,N=180.,1
repeat=''
renew=0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index("-fsa")
sampfile=sys.argv[ind+1]
if '-exc' in sys.argv:
Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt')
for crit in Crits:
if crit['pmag_criteria_code']=='DE-SPEC':
M=float(crit['specimen_mad'])
N=float(crit['specimen_n'])
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-N' in sys.argv: renew=1
#
if in_file[0]!="/":in_file=dir_path+'/'+in_file
if sampfile[0]!="/":sampfile=dir_path+'/'+sampfile
crd='s'
Specs,file_type=pmag.magic_read(in_file)
if file_type!='pmag_specimens':
print ' bad pmag_specimen input file'
sys.exit()
Samps,file_type=pmag.magic_read(sampfile)
if file_type!='er_samples':
print ' bad er_samples input file'
sys.exit()
SO_methods=[]
for rec in Samps:
if 'sample_orientation_flag' not in rec.keys(): rec['sample_orientation_flag']='g'
if 'sample_description' not in rec.keys(): rec['sample_description']=''
if renew==1:
rec['sample_orientation_flag']='g'
description=rec['sample_description']
if '#' in description:
newdesc=""
c=0
while description[c]!='#' and c<len(description)-1: # look for first pound sign
newdesc=newdesc+description[c]
c+=1
while description[c]=='#':
c+=1# skip first set of pound signs
while description[c]!='#':c+=1 # find second set of pound signs
while description[c]=='#' and c<len(description)-1:c+=1 # skip second set of pound signs
while c<len(description)-1: # look for first pound sign
newdesc=newdesc+description[c]
c+=1
rec['sample_description']=newdesc # edit out old comment about orientations
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth.strip() and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
pmag.magic_write(sampfile,Samps,'er_samples')
SO_priorities=pmag.set_priorities(SO_methods,0)
sitelist=[]
for rec in Specs:
if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
sitelist.sort()
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],5,5)
k=0
while k<len(sitelist):
site=sitelist[k]
print site
data=[]
ThisSiteSpecs=pmag.get_dictitem(Specs,'er_site_name',site,'T')
ThisSiteSpecs=pmag.get_dictitem(ThisSiteSpecs,'specimen_tilt_correction','-1','T') # get all the unoriented data
for spec in ThisSiteSpecs:
if spec['specimen_mad']!="" and spec['specimen_n']!="" and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N:
# good spec, now get orientation....
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",spec['er_sample_name']
orient["sample_azimuth"]=""
orient["sample_dip"]=""
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
if orient["sample_azimuth"] !="":
redo=0
p+=1
if orient['sample_azimuth']!="":
rec={}
for key in spec.keys():rec[key]=spec[key]
rec['dec'],rec['inc']=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(orient['sample_azimuth']),float(orient['sample_dip']))
rec["tilt_correction"]='1'
crd='g'
rec['sample_azimuth']=orient['sample_azimuth']
rec['sample_dip']=orient['sample_dip']
data.append(rec)
if len(data)>2:
print 'specimen, dec, inc, n_meas/MAD,| method codes '
for i in range(len(data)):
print '%s: %7.1f %7.1f %s / %s | %s' % (data[i]['er_specimen_name'], data[i]['dec'], data[i]['inc'], data[i]['specimen_n'], data[i]['specimen_mad'], data[i]['magic_method_codes'])
fpars=pmag.dolnp(data,'specimen_direction_type')
print "\n Site lines planes kappa a95 dec inc"
print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"]
if out_file!="":
if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff:
out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95']))
pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
pmagplotlib.drawFIGS(EQ)
if k!=0 and repeat!='y':
ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ")
elif k==0 and repeat!='y':
ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n ")
if ans=="p": k-=2
if ans=="a":
files={}
files['eqarea']=site+'_'+crd+'_eqarea'+'.'+fmt
pmagplotlib.saveP(EQ,files)
if ans=="q": sys.exit()
if ans=="e" and Samps==[]:
print "can't edit samples without orientation file, sorry"
elif ans=="e":
# k-=1
testspec=raw_input("Enter name of specimen to check: ")
for spec in data:
if spec['er_specimen_name']==testspec:
# first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i
d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,-float(spec['sample_dip']))
XY=pmag.dimap(d,i)
pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='g^')
# first test wrong end of compass (take az-180.)
d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,float(spec['sample_dip']))
XY=pmag.dimap(d,i)
pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='kv')
# did the sample spin in the hole?
# now spin around specimen's z
X_up,Y_up,X_d,Y_d=[],[],[],[]
for incr in range(0,360,5):
d,i=pmag.dogeo(float(spec['specimen_dec'])+incr,float(spec['specimen_inc']),float(spec['sample_azimuth']),float(spec['sample_dip']))
XY=pmag.dimap(d,i)
if i>=0:
X_d.append(XY[0])
Y_d.append(XY[1])
else:
X_up.append(XY[0])
Y_up.append(XY[1])
pmagplotlib.plotXY(EQ['eqarea'],X_d,Y_d,sym='b.')
pmagplotlib.plotXY(EQ['eqarea'],X_up,Y_up,sym='c.')
pmagplotlib.drawFIGS(EQ)
break
print "Triangle: wrong arrow for drill direction."
print "Delta: wrong end of compass."
print "Small circle: wrong mark on sample. [cyan upper hemisphere]"
deleteme=raw_input("Mark this sample as bad? y/[n] ")
if deleteme=='y':
reason=raw_input("Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other ")
if reason=='1':
description=' sample broke while drilling'
if reason=='2':
description=' wrong drill direction '
if reason=='3':
description=' wrong compass direction '
if reason=='4':
description=' bad mark in field'
if reason=='5':
description=' displaced block'
if reason=='6':
description=raw_input('Enter brief reason for deletion: ')
for samp in Samps:
if samp['er_sample_name']==spec['er_sample_name']:
samp['sample_orientation_flag']='b'
samp['sample_description']=samp['sample_description']+' ## direction deleted because: '+description+'##' # mark description
pmag.magic_write(sampfile,Samps,'er_samples')
repeat=raw_input("Mark another sample, this site? y/[n] ")
if repeat=='y': k-=1
else:
print 'skipping site - not enough data with specified coordinate system'
k+=1
print "sample flags stored in ",sampfile
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():
"""
NAME
nrm_specimens_magic.py
DESCRIPTION
converts NRM data in a magic_measurements type file to
geographic and tilt corrected data in a pmag_specimens type file
SYNTAX
nrm_specimens_magic.py [-h][command line options]
OPTIONS:
-h prints the help message and quits
-f MFILE: specify input file
-fsa SFILE: specify er_samples format file [with orientations]
-F PFILE: specify output file
-A do not average replicate measurements
-crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted)
NB: you must have the SFILE in this directory
DEFAULTS
MFILE: magic_measurements.txt
PFILE: nrm_specimens.txt
SFILE: er_samples.txt
coord: specimen
average replicate measurements?: YES
"""
#
# define some variables
#
beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
samp_file=1
args=sys.argv
geo,tilt,orient=0,0,0
doave=1
user,comment,doave,coord="","",1,""
dir_path='.'
if "-h" in args:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
meas_file=dir_path+"/magic_measurements.txt"
pmag_file=dir_path+"/nrm_specimens.txt"
samp_file=dir_path+"/er_samples.txt"
if "-A" in args: doave=0
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=dir_path+'/'+sys.argv[ind+1]
speclist=[]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=sys.argv[ind+1]
if coord=="g":
geo,orient=1,1
if coord=="t":
tilt,orient,geo=1,1,1
#
# read in data
if samp_file!="":
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print "This is not a valid er_samples file "
sys.exit()
else: print samp_file,' read in with ',len(samp_data),' records'
else:
print 'no orientations - will create file in specimen coordinates'
geo,tilt,orient=0,0,0
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
#
if orient==1:
# set orientation priorities
SO_methods=[]
orientation_priorities={'0':'SO-SUN','1':'SO-GPS-DIFF','2':'SO-SIGHT-BACK','3':'SO-CMD-NORTH','4':'SO-MAG'}
for rec in samp_data:
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
#
# sort the sample names
#
sids=pmag.get_specs(meas_data)
#
#
PmagSpecRecs=[]
for s in sids:
skip=0
recnum=0
PmagSpecRec={}
PmagSpecRec["er_analyst_mail_names"]=user
method_codes,inst_code=[],""
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth=[]
for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record
if rec["er_specimen_name"]==s:
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
PmagSpecRec["er_citation_names"]="This study"
PmagSpecRec["magic_instrument_codes"]=""
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
if len(rec["magic_instrument_codes"]) > len(inst_code):
inst_code=rec["magic_instrument_codes"]
PmagSpecRec["magic_instrument_codes"]=inst_code # copy over instruments
break
#
# now check for correct method labels for all measurements
#
nrm_data=[]
for meas_rec in meas_data:
if meas_rec['er_specimen_name']==PmagSpecRec['er_specimen_name']:
meths=meas_rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:meas_meth.append(meth)
if "LT-NO" in meas_meth:nrm_data.append(meas_rec)
#
data,units=pmag.find_dmag_rec(s,nrm_data)
#
datablock=data
#
# find replicate measurements at NRM step and average them
#
Specs=[]
if doave==1:
step_meth,avedata=pmag.vspec(data)
if len(avedata) != len(datablock):
method_codes.append("DE-VM")
SpecRec=avedata[0]
print 'averaging data '
else: SpecRec=data[0]
Specs.append(SpecRec)
else:
for spec in data:Specs.append(spec)
for SpecRec in Specs:
#
# do geo or stratigraphic correction now
#
if geo==1:
#
# find top priority orientation method
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="": method_codes.append(az_type)
redo=0
while redo==1:
if p>=len(orientation_priorities):
print "no orientation data for ",s
skip,redo=1,0
break
az_type=orientation_priorities[str(p)]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="":
method_codes.append(az_type.strip())
redo=0
elif orient["sample_azimuth"] =="":
p+=1
#
# if stratigraphic selected, get stratigraphic correction
#
if skip==0 and orient["sample_azimuth"]!="" and orient["sample_dip"]!="":
d_geo,i_geo=pmag.dogeo(SpecRec[1],SpecRec[2],orient["sample_azimuth"],orient["sample_dip"])
SpecRec[1]=d_geo
SpecRec[2]=i_geo
if tilt==1 and "sample_bed_dip" in orient.keys() and orient['sample_bed_dip']!="":
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"])
SpecRec[1]=d_tilt
SpecRec[2]=i_tilt
if skip==0:
PmagSpecRec["specimen_dec"]='%7.1f ' %(SpecRec[1])
PmagSpecRec["specimen_inc"]='%7.1f ' %(SpecRec[2])
if geo==1 and tilt==0:PmagSpecRec["specimen_tilt_correction"]='0'
if geo==1 and tilt==1: PmagSpecRec["specimen_tilt_correction"]='100'
if geo==0 and tilt==0: PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["magic_method_codes"]="LT-NO"
if len(method_codes) != 0:
methstring=""
for meth in method_codes:
methstring=methstring+ ":" +meth
PmagSpecRec["magic_method_codes"]=methstring[1:]
PmagSpecRec["specimen_description"]="NRM data"
PmagSpecRecs.append(PmagSpecRec)
pmag.magic_write(pmag_file,PmagSpecRecs,'pmag_specimens')
print "Data saved in ",pmag_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
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimens.txt file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
allows testing and reject specimens for bad orientations
SYNTAX
site_edit_magic.py [command line options]
OPTIONS
-h: prints help and quits
-f: specify pmag_specimen format file, default is pmag_specimens.txt
-fsa: specify er_samples.txt file
-exc: use existing pmag_criteria.txt file
-N: reset all sample flags to good
OUPUT
edited er_samples.txt file
"""
dir_path = '.'
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
in_file = 'pmag_specimens.txt'
sampfile = 'er_samples.txt'
out_file = ""
fmt, plot = 'svg', 1
Crits = ""
M, N = 180., 1
repeat = ''
renew = 0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
if '-fsa' in sys.argv:
ind = sys.argv.index("-fsa")
sampfile = sys.argv[ind + 1]
if '-exc' in sys.argv:
Crits, file_type = pmag.magic_read(dir_path + '/pmag_criteria.txt')
for crit in Crits:
if crit['pmag_criteria_code'] == 'DE-SPEC':
M = float(crit['specimen_mad'])
N = float(crit['specimen_n'])
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-N' in sys.argv: renew = 1
#
if in_file[0] != "/": in_file = dir_path + '/' + in_file
if sampfile[0] != "/": sampfile = dir_path + '/' + sampfile
crd = 's'
Specs, file_type = pmag.magic_read(in_file)
if file_type != 'pmag_specimens':
print(' bad pmag_specimen input file')
sys.exit()
Samps, file_type = pmag.magic_read(sampfile)
if file_type != 'er_samples':
print(' bad er_samples input file')
sys.exit()
SO_methods = []
for rec in Samps:
if 'sample_orientation_flag' not in list(rec.keys()):
rec['sample_orientation_flag'] = 'g'
if 'sample_description' not in list(rec.keys()):
rec['sample_description'] = ''
if renew == 1:
rec['sample_orientation_flag'] = 'g'
description = rec['sample_description']
if '#' in description:
newdesc = ""
c = 0
while description[c] != '#' and c < len(
description) - 1: # look for first pound sign
newdesc = newdesc + description[c]
c += 1
while description[c] == '#':
c += 1 # skip first set of pound signs
while description[c] != '#':
c += 1 # find second set of pound signs
while description[c] == '#' and c < len(description) - 1:
c += 1 # skip second set of pound signs
while c < len(description) - 1: # look for first pound sign
newdesc = newdesc + description[c]
c += 1
rec['sample_description'] = newdesc # edit out old comment about orientations
if "magic_method_codes" in rec:
methlist = rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth.strip() and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods:
SO_methods.append(meth.strip())
pmag.magic_write(sampfile, Samps, 'er_samples')
SO_priorities = pmag.set_priorities(SO_methods, 0)
sitelist = []
for rec in Specs:
if rec['er_site_name'] not in sitelist:
sitelist.append(rec['er_site_name'])
sitelist.sort()
EQ = {}
EQ['eqarea'] = 1
pmagplotlib.plot_init(EQ['eqarea'], 5, 5)
k = 0
while k < len(sitelist):
site = sitelist[k]
print(site)
data = []
ThisSiteSpecs = pmag.get_dictitem(Specs, 'er_site_name', site, 'T')
ThisSiteSpecs = pmag.get_dictitem(ThisSiteSpecs,
'specimen_tilt_correction', '-1',
'T') # get all the unoriented data
for spec in ThisSiteSpecs:
if spec['specimen_mad'] != "" and spec[
'specimen_n'] != "" and float(
spec['specimen_mad']) <= M and float(
spec['specimen_n']) >= N:
# good spec, now get orientation....
redo, p = 1, 0
if len(SO_methods) <= 1:
az_type = SO_methods[0]
orient = pmag.find_samp_rec(spec["er_sample_name"], Samps,
az_type)
redo = 0
while redo == 1:
if p >= len(SO_priorities):
print("no orientation data for ",
spec['er_sample_name'])
orient["sample_azimuth"] = ""
orient["sample_dip"] = ""
redo = 0
else:
az_type = SO_methods[SO_methods.index(
SO_priorities[p])]
orient = pmag.find_samp_rec(spec["er_sample_name"],
Samps, az_type)
if orient["sample_azimuth"] != "":
redo = 0
p += 1
if orient['sample_azimuth'] != "":
rec = {}
for key in list(spec.keys()):
rec[key] = spec[key]
rec['dec'], rec['inc'] = pmag.dogeo(
float(spec['specimen_dec']),
float(spec['specimen_inc']),
float(orient['sample_azimuth']),
float(orient['sample_dip']))
rec["tilt_correction"] = '1'
crd = 'g'
rec['sample_azimuth'] = orient['sample_azimuth']
rec['sample_dip'] = orient['sample_dip']
data.append(rec)
if len(data) > 2:
print('specimen, dec, inc, n_meas/MAD,| method codes ')
for i in range(len(data)):
print('%s: %7.1f %7.1f %s / %s | %s' %
(data[i]['er_specimen_name'], data[i]['dec'],
data[i]['inc'], data[i]['specimen_n'],
data[i]['specimen_mad'], data[i]['magic_method_codes']))
fpars = pmag.dolnp(data, 'specimen_direction_type')
print("\n Site lines planes kappa a95 dec inc")
print(site, fpars["n_lines"], fpars["n_planes"], fpars["K"],
fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"])
if out_file != "":
if float(fpars["alpha95"]) <= acutoff and float(
fpars["K"]) >= kcutoff:
out.write('%s %s %s\n' %
(fpars["dec"], fpars['inc'], fpars['alpha95']))
pmagplotlib.plot_lnp(EQ['eqarea'], site, data, fpars,
'specimen_direction_type')
pmagplotlib.draw_figs(EQ)
if k != 0 and repeat != 'y':
ans = input(
"s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n "
)
elif k == 0 and repeat != 'y':
ans = input(
"s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n "
)
if ans == "p": k -= 2
if ans == "a":
files = {}
files['eqarea'] = site + '_' + crd + '_eqarea' + '.' + fmt
pmagplotlib.save_plots(EQ, files)
if ans == "q": sys.exit()
if ans == "e" and Samps == []:
print("can't edit samples without orientation file, sorry")
elif ans == "e":
# k-=1
testspec = input("Enter name of specimen to check: ")
for spec in data:
if spec['er_specimen_name'] == testspec:
# first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i
d, i = pmag.dogeo(float(spec['specimen_dec']),
float(spec['specimen_inc']),
float(spec['sample_azimuth']) - 180.,
-float(spec['sample_dip']))
XY = pmag.dimap(d, i)
pmagplotlib.plot_xy(EQ['eqarea'], [XY[0]], [XY[1]],
sym='g^')
# first test wrong end of compass (take az-180.)
d, i = pmag.dogeo(float(spec['specimen_dec']),
float(spec['specimen_inc']),
float(spec['sample_azimuth']) - 180.,
float(spec['sample_dip']))
XY = pmag.dimap(d, i)
pmagplotlib.plot_xy(EQ['eqarea'], [XY[0]], [XY[1]],
sym='kv')
# did the sample spin in the hole?
# now spin around specimen's z
X_up, Y_up, X_d, Y_d = [], [], [], []
for incr in range(0, 360, 5):
d, i = pmag.dogeo(
float(spec['specimen_dec']) + incr,
float(spec['specimen_inc']),
float(spec['sample_azimuth']),
float(spec['sample_dip']))
XY = pmag.dimap(d, i)
if i >= 0:
X_d.append(XY[0])
Y_d.append(XY[1])
else:
X_up.append(XY[0])
Y_up.append(XY[1])
pmagplotlib.plot_xy(EQ['eqarea'], X_d, Y_d, sym='b.')
pmagplotlib.plot_xy(EQ['eqarea'], X_up, Y_up, sym='c.')
pmagplotlib.draw_figs(EQ)
break
print("Triangle: wrong arrow for drill direction.")
print("Delta: wrong end of compass.")
print(
"Small circle: wrong mark on sample. [cyan upper hemisphere]"
)
deleteme = input("Mark this sample as bad? y/[n] ")
if deleteme == 'y':
reason = input(
"Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other "
)
if reason == '1':
description = ' sample broke while drilling'
if reason == '2':
description = ' wrong drill direction '
if reason == '3':
description = ' wrong compass direction '
if reason == '4':
description = ' bad mark in field'
if reason == '5':
description = ' displaced block'
if reason == '6':
description = input(
'Enter brief reason for deletion: ')
for samp in Samps:
if samp['er_sample_name'] == spec['er_sample_name']:
samp['sample_orientation_flag'] = 'b'
samp['sample_description'] = samp[
'sample_description'] + ' ## direction deleted because: ' + description + '##' # mark description
pmag.magic_write(sampfile, Samps, 'er_samples')
repeat = input("Mark another sample, this site? y/[n] ")
if repeat == 'y': k -= 1
else:
print(
'skipping site - not enough data with specified coordinate system'
)
k += 1
print("sample flags stored in ", sampfile)
def main():
"""
NAME
zeq_magic_redo.py
DESCRIPTION
Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
SYNTAX
zeq_magic_redo.py [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-F: specify output file, default is zeq_specimens.txt
-fre REDO: specify redo file, default is "zeq_redo"
-fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt"
-A : don't average replicate measurements, default is yes
-crd [s,g,t] :
specify coordinate system [s,g,t] [default is specimen coordinates]
are specimen, geographic, and tilt corrected respectively
NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
INPUTS
zeq_redo format file is:
specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]
"""
dir_path='.'
INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data
beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
user,doave,comment= "",1,""
geo,tilt=0,0
version_num=pmag.get_version()
args=sys.argv
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo"
samp_file,coord=dir_path+"/"+"er_samples.txt",""
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-A" in args:doave=0
if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
if "-f" in args:
ind=args.index("-f")
meas_file=dir_path+'/'+sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=dir_path+'/'+sys.argv[ind+1]
if "-fre" in args:
ind=args.index("-fre")
mk_file=dir_path+"/"+args[ind+1]
try:
mk_f=open(mk_file,'r')
except:
print("Bad redo file")
sys.exit()
mkspec,skipped=[],[]
speclist=[]
for line in mk_f.readlines():
tmp=line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=sys.argv[ind+1]
if coord=="g":geo,tilt=1,0
if coord=="t":geo,tilt=1,1
#
# now get down to bidness
if geo==1:
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print(file_type)
print("This is not a valid er_samples file ")
sys.exit()
#
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(file_type)
print(file_type,"This is not a valid magic_measurements file ")
sys.exit()
#
# sort the specimen names
#
k = 0
print('Processing ',len(speclist), ' specimens - please wait')
PmagSpecs=[]
while k < len(speclist):
s=speclist[k]
recnum=0
PmagSpecRec={}
method_codes,inst_codes=[],[]
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth=[]
spec=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T')
if len(spec)==0:
print('no data found for specimen: ',s)
print('delete from zeq_redo input file...., then try again')
else:
for rec in spec: # copy of vital stats to PmagSpecRec from first spec record in demag block
skip=1
methods=rec["magic_method_codes"].split(":")
if len(set(methods) & set(INCL))>0:
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["magic_software_packages"]=version_num
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
if "er_expedition_name" in list(rec.keys()):PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
PmagSpecRec["er_citation_names"]="This study"
if "magic_experiment_name" not in list(rec.keys()): rec["magic_experiment_name"]=""
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
if "magic_instrument_codes" not in list(rec.keys()): rec["magic_instrument_codes"]=""
inst=rec['magic_instrument_codes'].split(":")
for I in inst:
if I not in inst_codes: # copy over instruments
inst_codes.append(I)
meths=rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:meas_meth.append(meth)
if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="T"
if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF")
if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="K"
if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T")
if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="J"
if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M")
#
#
datablock,units=pmag.find_dmag_rec(s,spec) # fish out the demag data for this specimen
#
if len(datablock) <2 or s not in speclist :
k+=1
# print 'skipping ', s,len(datablock)
else:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
#
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
#
# do geo or stratigraphic correction now
#
if geo==1 or tilt==1:
# find top priority orientation method
orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"])
if az_type not in method_codes:method_codes.append(az_type)
#
# if tilt selected, get stratigraphic correction
#
tiltblock,geoblock=[],[]
for rec in datablock:
if "sample_azimuth" in list(orient.keys()) and orient["sample_azimuth"]!="":
d_geo,i_geo=pmag.dogeo(rec[1],rec[2],float(orient["sample_azimuth"]),float(orient["sample_dip"]))
geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]])
if tilt==1 and "sample_bed_dip_direction" in list(orient.keys()):
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,float(orient["sample_bed_dip_direction"]),float(orient["sample_bed_dip"]))
tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]])
elif tilt==1:
if PmagSpecRec["er_sample_name"] not in skipped:
print('no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....')
skipped.append(PmagSpecRec["er_sample_name"])
else:
if PmagSpecRec["er_sample_name"] not in skipped:
print('no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....')
skipped.append(PmagSpecRec["er_sample_name"])
#
# get beg_pca, end_pca, pca
if PmagSpecRec['er_sample_name'] not in skipped:
compnum=-1
for spec in mkspec:
if spec[0]==s:
CompRec={}
for key in list(PmagSpecRec.keys()):CompRec[key]=PmagSpecRec[key]
compnum+=1
calculation_type=spec[1]
beg=float(spec[2])
end=float(spec[3])
if len(spec)>4:
comp_name=spec[4]
else:
comp_name=string.uppercase[compnum]
CompRec['specimen_comp_name']=comp_name
if beg < float(datablock[0][0]):beg=float(datablock[0][0])
if end > float(datablock[-1][0]):end=float(datablock[-1][0])
for l in range(len(datablock)):
if datablock[l][0]==beg:beg_pca=l
if datablock[l][0]==end:end_pca=l
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='0'
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='100'
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='-1'
if mpars["specimen_direction_type"]=="Error":
pass
else:
CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0])
try:
CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] )
except:
print('error in end_pca ',PmagSpecRec['er_specimen_name'])
CompRec["specimen_correction"]='u'
if calculation_type!='DE-FM':
CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"])
CompRec["specimen_alpha95"]=""
else:
CompRec["specimen_mad"]=""
CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"])
CompRec["specimen_n"]='%i '%(mpars["specimen_n"])
CompRec["specimen_dang"]='%7.1f '%(mpars["specimen_dang"])
CompMeths=[]
for meth in method_codes:
if meth not in CompMeths:CompMeths.append(meth)
if calculation_type not in CompMeths:CompMeths.append(calculation_type)
if geo==1: CompMeths.append("DA-DIR-GEO")
if tilt==1: CompMeths.append("DA-DIR-TILT")
if "DE-BFP" not in calculation_type:
CompRec["specimen_direction_type"]='l'
else:
CompRec["specimen_direction_type"]='p'
CompRec["magic_method_codes"]=""
if len(CompMeths) != 0:
methstring=""
for meth in CompMeths:
methstring=methstring+ ":" +meth
CompRec["magic_method_codes"]=methstring.strip(':')
CompRec["specimen_description"]=comment
if len(inst_codes) != 0:
inststring=""
for inst in inst_codes:
inststring=inststring+ ":" +inst
CompRec["magic_instrument_codes"]=inststring.strip(':')
PmagSpecs.append(CompRec)
k+=1
pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
print("Recalculated specimen data stored in ",pmag_file)
def main():
"""
NAME
zeq_magic.py
DESCRIPTION
reads in magic_measurements formatted file, makes plots of remanence decay
during demagnetization experiments. Reads in prior interpretations saved in
a pmag_specimens formatted file and allows re-interpretations of best-fit lines
and planes and saves (revised or new) interpretations in a pmag_specimens file.
interpretations are saved in the coordinate system used. Also allows judicious editting of
measurements to eliminate "bad" measurements. These are marked as such in the magic_measurements
input file. they are NOT deleted, just ignored.
SYNTAX
zeq_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEASFILE: sets magic_measurements format input file, default: magic_measurements.txt
-fsp SPECFILE: sets pmag_specimens format file with prior interpreations, default: zeq_specimens.txt
-Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
-crd [s,g,t]: sets coordinate system, g=geographic, t=tilt adjusted, default: specimen coordinate system
-fsa SAMPFILE: sets er_samples format file with orientation information, default: er_samples.txt
-spc SPEC plots single specimen SPEC, saves plot with specified format
with optional -dir settings and quits
-dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
beg: starting step for PCA calculation
end: ending step for PCA calculation
[L,P,F]: calculation type for line, plane or fisher mean
must be used with -spc option
-fmt FMT: set format of saved plot [png,svg,jpg]
-A: suppresses averaging of replicate measurements, default is to average
-sav: saves all plots without review
SCREEN OUTPUT:
Specimen, N, a95, StepMin, StepMax, Dec, Inc, calculation type
"""
# initialize some variables
doave,e,b=1,0,0 # average replicates, initial end and beginning step
plots,coord=0,'s'
noorient=0
version_num=pmag.get_version()
verbose=pmagplotlib.verbose
beg_pca,end_pca,direction_type="","",'l'
calculation_type,fmt="","svg"
user,spec_keys,locname="",[],''
plot_file=""
sfile=""
plot_file=""
PriorRecs=[] # empty list for prior interpretations
backup=0
specimen="" # can skip everything and just plot one specimen with bounds e,b
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
else:
dir_path='.'
inspec=dir_path+'/'+'zeq_specimens.txt'
meas_file,geo,tilt,ask,samp_file=dir_path+'/magic_measurements.txt',0,0,0,dir_path+'/er_samples.txt'
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=dir_path+'/'+sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
inspec=dir_path+'/'+sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
samp_file=dir_path+'/'+sys.argv[ind+1]
sfile='ok'
if '-crd' in sys.argv:
ind=sys.argv.index('-crd')
coord=sys.argv[ind+1]
if coord=='g' or coord=='t':
samp_data,file_type=pmag.magic_read(samp_file)
if file_type=='er_samples':sfile='ok'
geo=1
if coord=='t':tilt=1
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
specimen=sys.argv[ind+1]
if '-dir' in sys.argv:
ind=sys.argv.index('-dir')
direction_type=sys.argv[ind+1]
beg_pca=int(sys.argv[ind+2])
end_pca=int(sys.argv[ind+3])
if direction_type=='L':calculation_type='DE-BFL'
if direction_type=='P':calculation_type='DE-BFP'
if direction_type=='F':calculation_type='DE-FM'
if '-Fp' in sys.argv:
ind=sys.argv.index('-Fp')
plot_file=dir_path+'/'+sys.argv[ind+1]
if '-A' in sys.argv: doave=0
if '-sav' in sys.argv:
plots=1
verbose=0
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
#
first_save=1
meas_data,file_type=pmag.magic_read(meas_file)
changeM,changeS=0,0 # check if data or interpretations have changed
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
for rec in meas_data:
if "magic_method_codes" not in rec.keys(): rec["magic_method_codes"]=""
methods=""
tmp=rec["magic_method_codes"].replace(" ","").split(":")
for meth in tmp:
methods=methods+meth+":"
rec["magic_method_codes"]=methods[:-1] # get rid of annoying spaces in Anthony's export files
if "magic_instrument_codes" not in rec.keys() :rec["magic_instrument_codes"]=""
PriorSpecs=[]
PriorRecs,file_type=pmag.magic_read(inspec)
if len(PriorRecs)==0:
if verbose:print "starting new file ",inspec
for Rec in PriorRecs:
if 'magic_software_packages' not in Rec.keys():Rec['magic_software_packages']=""
if Rec['er_specimen_name'] not in PriorSpecs:
if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A"
PriorSpecs.append(Rec['er_specimen_name'])
else:
if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A"
if "magic_method_codes" in Rec.keys():
methods=[]
tmp=Rec["magic_method_codes"].replace(" ","").split(":")
for meth in tmp:
methods.append(meth)
if 'DE-FM' in methods:
Rec['calculation_type']='DE-FM' # this won't be imported but helps
if 'DE-BFL' in methods:
Rec['calculation_type']='DE-BFL'
if 'DE-BFL-A' in methods:
Rec['calculation_type']='DE-BFL-A'
if 'DE-BFL-O' in methods:
Rec['calculation_type']='DE-BFL-O'
if 'DE-BFP' in methods:
Rec['calculation_type']='DE-BFP'
else:
Rec['calculation_type']='DE-BFL' # default is to assume a best-fit line
#
# get list of unique specimen names
#
sids=pmag.get_specs(meas_data)
#
# set up plots, angle sets X axis to horizontal, direction_type 'l' is best-fit line
# direction_type='p' is great circle
#
#
# draw plots for sample s - default is just to step through zijderveld diagrams
#
#
# define figure numbers for equal area, zijderveld,
# and intensity vs. demagnetiztion step respectively
ZED={}
ZED['eqarea'],ZED['zijd'], ZED['demag']=1,2,3
pmagplotlib.plot_init(ZED['eqarea'],5,5)
pmagplotlib.plot_init(ZED['zijd'],6,5)
pmagplotlib.plot_init(ZED['demag'],5,5)
save_pca=0
if specimen=="":
k = 0
else:
k=sids.index(specimen)
angle,direction_type="",""
setangle=0
CurrRecs=[]
while k < len(sids):
CurrRecs=[]
if setangle==0:angle=""
method_codes,inst_code=[],""
s=sids[k]
PmagSpecRec={}
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec['magic_software_packages']=version_num
PmagSpecRec['specimen_description']=""
PmagSpecRec['magic_method_codes']=""
if verbose and s!="":print s, k , 'out of ',len(sids)
#
# collect info for the PmagSpecRec dictionary
#
s_meas=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T') # fish out this specimen
s_meas=pmag.get_dictitem(s_meas,'magic_method_codes','Z','has') # fish out zero field steps
if len(s_meas)>0:
for rec in s_meas: # fix up a few things for the output record
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"] # copy over instruments
PmagSpecRec["er_citation_names"]="This study"
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
locname=rec['er_location_name']
if 'er_expedition_name' in rec.keys(): PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
PmagSpecRec["magic_method_codes"]=rec["magic_method_codes"]
if "magic_experiment_name" not in rec.keys():
PmagSpecRec["magic_experiment_names"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
break
#
# find the data from the meas_data file for this specimen
#
data,units=pmag.find_dmag_rec(s,meas_data)
PmagSpecRec["measurement_step_unit"]= units
u=units.split(":")
if "T" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-AF"
if "K" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-T"
if "J" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-M"
#
# find prior interpretation
#
if len(CurrRecs)==0: # check if already in
beg_pca,end_pca="",""
calculation_type=""
if inspec !="":
if verbose: print " looking up previous interpretations..."
precs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'T') # get all the prior recs with this specimen name
precs=pmag.get_dictitem(precs,'magic_method_codes','LP-DIR','has') # get the directional data
PriorRecs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'F') # take them all out of prior recs
# get the ones that meet the current coordinate system
for prec in precs:
if 'specimen_tilt_correction' not in prec.keys() or prec['specimen_tilt_correction']=='-1':
crd='s'
elif prec['specimen_tilt_correction']=='0':
crd='g'
elif prec['specimen_tilt_correction']=='100':
crd='t'
else:
crd='?'
CurrRec={}
for key in prec.keys():CurrRec[key]=prec[key]
CurrRecs.append(CurrRec) # put in CurrRecs
method_codes= CurrRec["magic_method_codes"].replace(" ","").split(':')
calculation_type='DE-BFL'
if 'DE-FM' in method_codes: calculation_type='DE-FM'
if 'DE-BFP' in method_codes: calculation_type='DE-BFP'
if 'DE-BFL-A' in method_codes: calculation_type='DE-BFL-A'
if 'specimen_dang' not in CurrRec.keys():
if verbose:print 'Run mk_redo.py and zeq_magic_redo.py to get the specimen_dang values'
CurrRec['specimen_dang']=-1
if calculation_type!='DE-FM' and crd==coord: # not a fisher mean
if verbose:print "Specimen N MAD DANG start end dec inc type component coordinates"
if units=='K':
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif units=='T':
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif 'T' in units and 'K' in units:
if float(CurrRec['measurement_step_min'])<1.0 :
min=float(CurrRec['measurement_step_min'])*1e3
else:
min=float(CurrRec['measurement_step_min'])-273
if float(CurrRec['measurement_step_max'])<1.0 :
max=float(CurrRec['measurement_step_max'])*1e3
else:
max=float(CurrRec['measurement_step_max'])-273
if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s %s\n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd)
elif 'J' in units:
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif calculation_type=='DE-FM' and crd==coord: # fisher mean
if verbose:print "Specimen a95 DANG start end dec inc type component coordinates"
if units=='K':
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif units=='T':
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif 'T' in units and 'K' in units:
if float(CurrRec['measurement_step_min'])<1.0 :
min=float(CurrRec['measurement_step_min'])*1e3
else:
min=float(CurrRec['measurement_step_min'])-273
if float(CurrRec['measurement_step_max'])<1.0 :
max=float(CurrRec['measurement_step_max'])*1e3
else:
max=float(CurrRec['measurement_step_max'])-273
if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd)
elif 'J' in units:
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
if len(CurrRecs)==0:beg_pca,end_pca="",""
datablock=data
noskip=1
if len(datablock) <3:
noskip=0
if backup==0:
k+=1
else:
k-=1
if len(CurrRecs)>0:
for rec in CurrRecs:
PriorRecs.append(rec)
CurrRecs=[]
else:
backup=0
if noskip:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
# #
# do geo or stratigraphic correction now
#
if geo==1:
#
# find top priority orientation method
orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"])
if az_type=='SO-NO':
if verbose: print "no orientation data for ",s
orient["sample_azimuth"]=0
orient["sample_dip"]=0
noorient=1
method_codes.append("SO-NO")
orient["sample_azimuth"]=0
orient["sample_dip"]=0
orient["sample_bed_dip_azimuth"]=0
orient["sample_bed_dip"]=0
noorient=1
method_codes.append("SO-NO")
else:
noorient=0
#
# if stratigraphic selected, get stratigraphic correction
#
tiltblock,geoblock=[],[]
for rec in datablock:
d_geo,i_geo=pmag.dogeo(rec[1],rec[2],float(orient["sample_azimuth"]),float(orient["sample_dip"]))
geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5],rec[6]])
if tilt==1 and "sample_bed_dip" in orient.keys() and float(orient['sample_bed_dip'])!=0:
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,float(orient["sample_bed_dip_direction"]),float(orient["sample_bed_dip"]))
tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5],rec[6]])
if tilt==1: plotblock=tiltblock
if geo==1 and tilt==0:plotblock=geoblock
if geo==0 and tilt==0: plotblock=datablock
#
# set the end pca point to last point if not set
if e==0 or e>len(plotblock)-1: e=len(plotblock)-1
if angle=="": angle=plotblock[0][1] # rotate to NRM declination
title=s+'_s'
if geo==1 and tilt==0 and noorient!=1:title=s+'_g'
if tilt==1 and noorient!=1:title=s+'_t'
pmagplotlib.plotZED(ZED,plotblock,angle,title,units)
if verbose:pmagplotlib.drawFIGS(ZED)
if len(CurrRecs)!=0:
for prec in CurrRecs:
if 'calculation_type' not in prec.keys():
calculation_type=''
else:
calculation_type=prec["calculation_type"]
direction_type=prec["specimen_direction_type"]
if calculation_type !="":
beg_pca,end_pca="",""
for j in range(len(datablock)):
if data[j][0]==float(prec["measurement_step_min"]):beg_pca=j
if data[j][0]==float(prec["measurement_step_max"]):end_pca=j
if beg_pca=="" or end_pca=="":
if verbose:
print "something wrong with prior interpretation "
break
if calculation_type!="":
if beg_pca=="":beg_pca=0
if end_pca=="":end_pca=len(plotblock)-1
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
pmagplotlib.plotDir(ZED,mpars,geoblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
pmagplotlib.plotDir(ZED,mpars,tiltblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
pmagplotlib.plotDir(ZED,mpars,plotblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
#
# print out data for this sample to screen
#
recnum=0
for plotrec in plotblock:
if units=='T' and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6])
if units=="K" and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
if units=="J" and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0],' J',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
if 'K' in units and 'T' in units:
if plotrec[0]>=1. and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
if plotrec[0]<1. and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6])
recnum += 1
if specimen!="":
if plot_file=="":
basename=locname+'_'+s
else:
basename=plot_file
files={}
for key in ZED.keys():
files[key]=basename+'_'+key+'.'+fmt
pmagplotlib.saveP(ZED,files)
sys.exit()
else: # interactive
if plots==0:
ans='b'
k+=1
changeS=0
while ans != "":
if len(CurrRecs)==0:
print """
g/b: indicates good/bad measurement. "bad" measurements excluded from calculation
set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen,
change [h]orizontal projection angle, change [c]oordinate systems,
[e]dit data, [q]uit:
"""
else:
print """
g/b: indicates good/bad measurement. "bad" measurements excluded from calculation
set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen,
change [h]orizontal projection angle, change [c]oordinate systems,
[d]elete current interpretation(s), [e]dit data, [q]uit:
"""
ans=raw_input('<Return> for next specimen \n')
setangle=0
if ans=='d': # delete this interpretation
CurrRecs=[]
k-=1 # replot same specimen
ans=""
changeS=1
if ans=='q':
if changeM==1:
ans=raw_input('Save changes to magic_measurements.txt? y/[n] ')
if ans=='y':
pmag.magic_write(meas_file,meas_data,'magic_measurements')
print "Good bye"
sys.exit()
if ans=='a':
if plot_file=="":
basename=locname+'_'+s+'_'
else:
basename=plot_file
files={}
for key in ZED.keys():
files[key]=basename+'_'+coord+'_'+key+'.'+fmt
pmagplotlib.saveP(ZED,files)
ans=""
if ans=='p':
k-=2
ans=""
backup=1
if ans=='c':
k-=1 # replot same block
if tilt==0 and geo ==1:print "You are currently viewing geographic coordinates "
if tilt==1 and geo ==1:print "You are currently viewing stratigraphic coordinates "
if tilt==0 and geo ==0: print "You are currently viewing sample coordinates "
print "\n Which coordinate system do you wish to view? "
coord=raw_input(" <Return> specimen, [g] geographic, [t] tilt corrected ")
if coord=="g":geo,tilt=1,0
if coord=="t":
geo=1
tilt=1
if coord=="":
coord='s'
geo=0
tilt=0
if geo==1 and sfile=="":
samp_file=raw_input(" Input er_samples file for sample orientations [er_samples.txt] " )
if samp_file=="":samp_file="er_samples.txt"
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print "This is not a valid er_samples file - coordinate system not changed"
else:
sfile="ok"
ans=""
if ans=='s':
keepon=1
sample=raw_input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
k =sids.index(sample)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if sample in sids[qq]:tmplist.append(sids[qq])
print sample," not found, but this was: "
print tmplist
sample=raw_input('Select one or try again\n ')
angle,direction_type="",""
setangle=0
ans=""
if ans=='h':
k-=1
angle=raw_input("Enter desired declination for X axis 0-360 ")
angle=float(angle)
if angle==0:angle=0.001
s=sids[k]
setangle=1
ans=""
if ans=='e':
k-=1
ans=""
recnum=0
for plotrec in plotblock:
if plotrec[0]<=200 and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2])
if plotrec[0]>200 and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2])
recnum += 1
answer=raw_input('Enter index of point to change from bad to good or vice versa: ')
try:
ind=int(answer)
meas_data=pmag.mark_dmag_rec(s,ind,meas_data)
changeM=1
except:
'bad entry, try again'
if ans=='b':
if end_pca=="":end_pca=len(plotblock)-1
if beg_pca=="":beg_pca=0
k-=1 # stay on same sample until through
GoOn=0
while GoOn==0:
print 'Enter index of first point for pca: ','[',beg_pca,']'
answer=raw_input('return to keep default ')
if answer != "":
beg_pca=int(answer)
print 'Enter index of last point for pca: ','[',end_pca,']'
answer=raw_input('return to keep default ')
try:
end_pca=int(answer)
if plotblock[beg_pca][5]=='b' or plotblock[end_pca][5]=='b':
print "Can't select 'bad' measurement for PCA bounds -try again"
end_pca=len(plotblock)-1
beg_pca=0
elif beg_pca >=0 and beg_pca<=len(plotblock)-2 and end_pca>0 and end_pca<len(plotblock):
GoOn=1
else:
print beg_pca,end_pca, " are bad entry of indices - try again"
end_pca=len(plotblock)-1
beg_pca=0
except:
print beg_pca,end_pca, " are bad entry of indices - try again"
end_pca=len(plotblock)-1
beg_pca=0
GoOn=0
while GoOn==0:
if calculation_type!="":
print "Prior calculation type = ",calculation_type
ct=raw_input('Enter new Calculation Type: best-fit line, plane or fisher mean [l]/p/f : ' )
if ct=="" or ct=="l":
direction_type="l"
calculation_type="DE-BFL"
GoOn=1
elif ct=='p':
direction_type="p"
calculation_type="DE-BFP"
GoOn=1
elif ct=='f':
direction_type="l"
calculation_type="DE-FM"
GoOn=1
else:
print "bad entry of calculation type: try again. "
pmagplotlib.plotZED(ZED,plotblock,angle,s,units)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars['specimen_direction_type']=='Error':break
PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
if "SO-NO" not in method_codes:
PmagSpecRec["specimen_tilt_correction"]='0'
method_codes.append("DA-DIR-GEO")
else:
PmagSpecRec["specimen_tilt_correction"]='-1'
pmagplotlib.plotDir(ZED,mpars,geoblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars['specimen_direction_type']=='Error':break
PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
if "SO-NO" not in method_codes:
PmagSpecRec["specimen_tilt_correction"]='100'
method_codes.append("DA-DIR-TILT")
else:
PmagSpecRec["specimen_tilt_correction"]='-1'
pmagplotlib.plotDir(ZED,mpars,tiltblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars['specimen_direction_type']=='Error':break
PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
pmagplotlib.plotDir(ZED,mpars,plotblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
PmagSpecRec["measurement_step_min"]='%8.3e ' %(mpars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e ' %(mpars["measurement_step_max"])
PmagSpecRec["specimen_correction"]='u'
PmagSpecRec["specimen_dang"]='%7.1f ' %(mpars['specimen_dang'])
print 'DANG: ',PmagSpecRec["specimen_dang"]
if calculation_type!='DE-FM':
PmagSpecRec["specimen_mad"]='%7.1f ' %(mpars["specimen_mad"])
PmagSpecRec["specimen_alpha95"]=""
else:
PmagSpecRec["specimen_alpha95"]='%7.1f ' %(mpars["specimen_alpha95"])
PmagSpecRec["specimen_mad"]=""
PmagSpecRec["specimen_n"]='%i ' %(mpars["specimen_n"])
PmagSpecRec["specimen_direction_type"]=direction_type
PmagSpecRec["calculation_type"]=calculation_type # redundant and won't be imported - just for convenience
method_codes=PmagSpecRec["magic_method_codes"].split(':')
if len(method_codes) != 0:
methstring=""
for meth in method_codes:
ctype=meth.split('-')
if 'DE' not in ctype:methstring=methstring+ ":" +meth # don't include old direction estimation methods
methstring=methstring+':'+calculation_type
PmagSpecRec["magic_method_codes"]= methstring.strip(':')
print 'Method codes: ',PmagSpecRec['magic_method_codes']
if calculation_type!='DE-FM':
if units=='K':
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
elif units== 'T':
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
elif 'T' in units and 'K' in units:
if float(PmagSpecRec['measurement_step_min'])<1.0 :
min=float(PmagSpecRec['measurement_step_min'])*1e3
else:
min=float(PmagSpecRec['measurement_step_min'])-273
if float(PmagSpecRec['measurement_step_max'])<1.0 :
max=float(PmagSpecRec['measurement_step_max'])*1e3
else:
max=float(PmagSpecRec['measurement_step_max'])-273
print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
else:
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
else:
if 'K' in units:
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
elif 'T' in units:
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
elif 'T' in units and 'K' in units:
if float(PmagSpecRec['measurement_step_min'])<1.0 :
min=float(PmagSpecRec['measurement_step_min'])*1e3
else:
min=float(PmagSpecRec['measurement_step_min'])-273
if float(PmagSpecRec['measurement_step_max'])<1.0 :
max=float(PmagSpecRec['measurement_step_max'])*1e3
else:
max=float(PmagSpecRec['measurement_step_max'])-273
print '%s %i %7.1f %i %i %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
else:
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
saveit=raw_input("Save this interpretation? [y]/n \n")
if saveit!="n":
changeS=1
#
# put in details
#
angle,direction_type,setangle="","",0
if len(CurrRecs)>0:
replace=raw_input(" [0] add new component, or [1] replace existing interpretation(s) [default is replace] ")
if replace=="1" or replace=="":
CurrRecs=[]
PmagSpecRec['specimen_comp_name']='A'
CurrRecs.append(PmagSpecRec)
else:
print 'These are the current component names for this specimen: '
for trec in CurrRecs:print trec['specimen_comp_name']
compnum=raw_input("Enter new component name: ")
PmagSpecRec['specimen_comp_name']=compnum
print "Adding new component: ",PmagSpecRec['specimen_comp_name']
CurrRecs.append(PmagSpecRec)
else:
PmagSpecRec['specimen_comp_name']='A'
CurrRecs.append(PmagSpecRec)
k+=1
ans=""
else:
ans=""
else: # plots=1
k+=1
files={}
locname.replace('/','-')
print PmagSpecRec
for key in ZED.keys():
files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_'+coord+'_TY:_'+key+'_.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['demag']='DeMag Plot'
titles['zijd']='Zijderveld Plot'
titles['eqarea']='Equal Area Plot'
ZED = pmagplotlib.addBorders(ZED,titles,black,purple)
pmagplotlib.saveP(ZED,files)
if len(CurrRecs)>0:
for rec in CurrRecs: PriorRecs.append(rec)
if changeS==1:
if len(PriorRecs)>0:
save_redo(PriorRecs,inspec)
else:
os.system('rm '+inspec)
CurrRecs,beg_pca,end_pca=[],"","" # next up
changeS=0
else: k+=1 # skip record - not enough data
if changeM==1:
pmag.magic_write(meas_file,meas_data,'magic_measurements')
def main():
"""
NAME
zeq_magic_redo.py
DESCRIPTION
Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
SYNTAX
zeq_magic_redo.py [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-F: specify output file, default is zeq_specimens.txt
-fre REDO: specify redo file, default is "zeq_redo"
-fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt"
-A : don't average replicate measurements, default is yes
-crd [s,g,t] :
specify coordinate system [s,g,t] [default is specimen coordinates]
are specimen, geographic, and tilt corrected respectively
NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
INPUTS
zeq_redo format file is:
specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]
"""
dir_path = '.'
INCL = ["LT-NO", "LT-AF-Z", "LT-T-Z", "LT-M-Z"] # looking for demag data
beg, end, pole, geo, tilt, askave, save = 0, 0, [], 0, 0, 0, 0
user, doave, comment = "", 1, ""
geo, tilt = 0, 0
version_num = pmag.get_version()
args = sys.argv
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
meas_file, pmag_file, mk_file = dir_path + "/" + "magic_measurements.txt", dir_path + "/" + "zeq_specimens.txt", dir_path + "/" + "zeq_redo"
samp_file, coord = dir_path + "/" + "er_samples.txt", ""
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = sys.argv[ind + 1]
if "-A" in args: doave = 0
if "-leg" in args:
comment = "Recalculated from original measurements; supercedes published results. "
if "-f" in args:
ind = args.index("-f")
meas_file = dir_path + '/' + sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
pmag_file = dir_path + '/' + sys.argv[ind + 1]
if "-fre" in args:
ind = args.index("-fre")
mk_file = dir_path + "/" + args[ind + 1]
try:
mk_f = open(mk_file, 'r')
except:
print("Bad redo file")
sys.exit()
mkspec, skipped = [], []
speclist = []
for line in mk_f.readlines():
tmp = line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + '/' + sys.argv[ind + 1]
if "-crd" in args:
ind = args.index("-crd")
coord = sys.argv[ind + 1]
if coord == "g": geo, tilt = 1, 0
if coord == "t": geo, tilt = 1, 1
#
# now get down to bidness
if geo == 1:
samp_data, file_type = pmag.magic_read(samp_file)
if file_type != 'er_samples':
print(file_type)
print("This is not a valid er_samples file ")
sys.exit()
#
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(file_type)
print(file_type, "This is not a valid magic_measurements file ")
sys.exit()
#
# sort the specimen names
#
k = 0
print('Processing ', len(speclist), ' specimens - please wait')
PmagSpecs = []
while k < len(speclist):
s = speclist[k]
recnum = 0
PmagSpecRec = {}
method_codes, inst_codes = [], []
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth = []
spec = pmag.get_dictitem(meas_data, 'er_specimen_name', s, 'T')
if len(spec) == 0:
print('no data found for specimen: ', s)
print('delete from zeq_redo input file...., then try again')
else:
for rec in spec: # copy of vital stats to PmagSpecRec from first spec record in demag block
skip = 1
methods = rec["magic_method_codes"].split(":")
if len(set(methods) & set(INCL)) > 0:
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["magic_software_packages"] = version_num
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
if "er_expedition_name" in list(rec.keys()):
PmagSpecRec["er_expedition_name"] = rec[
"er_expedition_name"]
PmagSpecRec["er_citation_names"] = "This study"
if "magic_experiment_name" not in list(rec.keys()):
rec["magic_experiment_name"] = ""
PmagSpecRec["magic_experiment_names"] = rec[
"magic_experiment_name"]
if "magic_instrument_codes" not in list(rec.keys()):
rec["magic_instrument_codes"] = ""
inst = rec['magic_instrument_codes'].split(":")
for I in inst:
if I not in inst_codes: # copy over instruments
inst_codes.append(I)
meths = rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:
meas_meth.append(meth)
if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"] = "T"
if "LP-DIR-AF" not in method_codes:
method_codes.append("LP-DIR-AF")
if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"] = "K"
if "LP-DIR-T" not in method_codes:
method_codes.append("LP-DIR-T")
if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"] = "J"
if "LP-DIR-M" not in method_codes:
method_codes.append("LP-DIR-M")
#
#
datablock, units = pmag.find_dmag_rec(
s, spec) # fish out the demag data for this specimen
#
if len(datablock) < 2 or s not in speclist:
k += 1
# print 'skipping ', s,len(datablock)
else:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
#
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
#
# do geo or stratigraphic correction now
#
if geo == 1 or tilt == 1:
# find top priority orientation method
orient, az_type = pmag.get_orient(
samp_data, PmagSpecRec["er_sample_name"])
if az_type not in method_codes: method_codes.append(az_type)
#
# if tilt selected, get stratigraphic correction
#
tiltblock, geoblock = [], []
for rec in datablock:
if "sample_azimuth" in list(
orient.keys()) and orient["sample_azimuth"] != "":
d_geo, i_geo = pmag.dogeo(
rec[1], rec[2], float(orient["sample_azimuth"]),
float(orient["sample_dip"]))
geoblock.append(
[rec[0], d_geo, i_geo, rec[3], rec[4], rec[5]])
if tilt == 1 and "sample_bed_dip_direction" in list(
orient.keys()):
d_tilt, i_tilt = pmag.dotilt(
d_geo, i_geo,
float(orient["sample_bed_dip_direction"]),
float(orient["sample_bed_dip"]))
tiltblock.append([
rec[0], d_tilt, i_tilt, rec[3], rec[4], rec[5]
])
elif tilt == 1:
if PmagSpecRec["er_sample_name"] not in skipped:
print('no tilt correction for ',
PmagSpecRec["er_sample_name"],
' skipping....')
skipped.append(PmagSpecRec["er_sample_name"])
else:
if PmagSpecRec["er_sample_name"] not in skipped:
print('no geographic correction for ',
PmagSpecRec["er_sample_name"],
' skipping....')
skipped.append(PmagSpecRec["er_sample_name"])
#
# get beg_pca, end_pca, pca
if PmagSpecRec['er_sample_name'] not in skipped:
compnum = -1
for spec in mkspec:
if spec[0] == s:
CompRec = {}
for key in list(PmagSpecRec.keys()):
CompRec[key] = PmagSpecRec[key]
compnum += 1
calculation_type = spec[1]
beg = float(spec[2])
end = float(spec[3])
if len(spec) > 4:
comp_name = spec[4]
else:
comp_name = string.uppercase[compnum]
CompRec['specimen_comp_name'] = comp_name
if beg < float(datablock[0][0]):
beg = float(datablock[0][0])
if end > float(datablock[-1][0]):
end = float(datablock[-1][0])
for l in range(len(datablock)):
if datablock[l][0] == beg: beg_pca = l
if datablock[l][0] == end: end_pca = l
if geo == 1 and tilt == 0:
mpars = pmag.domean(geoblock, beg_pca, end_pca,
calculation_type)
if mpars["specimen_direction_type"] != "Error":
CompRec["specimen_dec"] = '%7.1f ' % (
mpars["specimen_dec"])
CompRec["specimen_inc"] = '%7.1f ' % (
mpars["specimen_inc"])
CompRec["specimen_tilt_correction"] = '0'
if geo == 1 and tilt == 1:
mpars = pmag.domean(tiltblock, beg_pca, end_pca,
calculation_type)
if mpars["specimen_direction_type"] != "Error":
CompRec["specimen_dec"] = '%7.1f ' % (
mpars["specimen_dec"])
CompRec["specimen_inc"] = '%7.1f ' % (
mpars["specimen_inc"])
CompRec["specimen_tilt_correction"] = '100'
if geo == 0 and tilt == 0:
mpars = pmag.domean(datablock, beg_pca, end_pca,
calculation_type)
if mpars["specimen_direction_type"] != "Error":
CompRec["specimen_dec"] = '%7.1f ' % (
mpars["specimen_dec"])
CompRec["specimen_inc"] = '%7.1f ' % (
mpars["specimen_inc"])
CompRec["specimen_tilt_correction"] = '-1'
if mpars["specimen_direction_type"] == "Error":
pass
else:
CompRec["measurement_step_min"] = '%8.3e ' % (
datablock[beg_pca][0])
try:
CompRec["measurement_step_max"] = '%8.3e ' % (
datablock[end_pca][0])
except:
print('error in end_pca ',
PmagSpecRec['er_specimen_name'])
CompRec["specimen_correction"] = 'u'
if calculation_type != 'DE-FM':
CompRec["specimen_mad"] = '%7.1f ' % (
mpars["specimen_mad"])
CompRec["specimen_alpha95"] = ""
else:
CompRec["specimen_mad"] = ""
CompRec["specimen_alpha95"] = '%7.1f ' % (
mpars["specimen_alpha95"])
CompRec["specimen_n"] = '%i ' % (
mpars["specimen_n"])
CompRec["specimen_dang"] = '%7.1f ' % (
mpars["specimen_dang"])
CompMeths = []
for meth in method_codes:
if meth not in CompMeths:
CompMeths.append(meth)
if calculation_type not in CompMeths:
CompMeths.append(calculation_type)
if geo == 1: CompMeths.append("DA-DIR-GEO")
if tilt == 1: CompMeths.append("DA-DIR-TILT")
if "DE-BFP" not in calculation_type:
CompRec["specimen_direction_type"] = 'l'
else:
CompRec["specimen_direction_type"] = 'p'
CompRec["magic_method_codes"] = ""
if len(CompMeths) != 0:
methstring = ""
for meth in CompMeths:
methstring = methstring + ":" + meth
CompRec[
"magic_method_codes"] = methstring.strip(
':')
CompRec["specimen_description"] = comment
if len(inst_codes) != 0:
inststring = ""
for inst in inst_codes:
inststring = inststring + ":" + inst
CompRec[
"magic_instrument_codes"] = inststring.strip(
':')
PmagSpecs.append(CompRec)
k += 1
pmag.magic_write(pmag_file, PmagSpecs, 'pmag_specimens')
print("Recalculated specimen data stored in ", pmag_file)
def main():
"""
NAME
nrm_specimens_magic.py
DESCRIPTION
converts NRM data in a measurements type file to
geographic and tilt corrected data in a specimens type file
SYNTAX
nrm_specimens_magic.py [-h][command line options]
OPTIONS:
-h prints the help message and quits
-f MFILE: specify input file
-fsa SFILE: specify samples format file [with orientations]
-F PFILE: specify output file
-A do not average replicate measurements
-crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted)
NB: you must have the SFILE in this directory
DEFAULTS
MFILE: measurements.txt
PFILE: nrm_specimens.txt
SFILE: samples.txt
coord: g
average replicate measurements?: YES
"""
#
# define some variables
#
beg, end, pole, geo, tilt, askave, save = 0, 0, [], 0, 0, 0, 0
samp_file = 1
args = sys.argv
geo, tilt, orient = 0, 0, 0
doave = 1
user, comment, doave, coord = "", "", 1, "g"
geo, orient = 1, 1
dir_path = '.'
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
meas_file = dir_path + "/measurements.txt"
spec_file = dir_path + "/specimens.txt"
samp_file = dir_path + "/samples.txt"
out_file = dir_path + "/nrm_specimens.txt"
if "-A" in args:
doave = 0
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
out_file = dir_path + '/' + sys.argv[ind + 1]
speclist = []
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + '/' + sys.argv[ind + 1]
if "-crd" in args:
ind = args.index("-crd")
coord = sys.argv[ind + 1]
if coord == "t":
tilt, orient, geo = 1, 1, 1
#
# read in data
#
meas_data = pd.read_csv(meas_file, header=1, sep='\t')
meas_data = meas_data[meas_data['method_codes'].str.contains('LT-NO') ==
True] # fish out NRM data
meas_data = meas_data[['specimen', 'dir_dec', 'dir_inc']]
meas_data = meas_data.dropna(subset=['dir_dec', 'dir_inc'])
meas_data = pd.DataFrame(meas_data)
# import samples for orientation info
#
##
if orient == 1:
spec_data = pd.read_csv(spec_file, header=1, sep='\t')
spec_data = spec_data[['specimen', 'sample']]
meas_data = pd.merge(meas_data,
spec_data,
how='inner',
on=['specimen'])
samp_data = pd.read_csv(samp_file, header=1, sep='\t')
#
sids = meas_data.specimen.unique() # list of specimen names
#
#
NrmSpecRecs = []
for spec in sids:
gdec, ginc, bdec, binc = "", "", "", ""
this_spec_data = meas_data[meas_data.specimen.str.contains(spec)]
this_sample = this_spec_data['sample'].iloc[-1]
this_sample_data = samp_data[samp_data['sample'].str.contains(
this_sample)]
this_sample_data = this_sample_data.to_dict('records')
for m in this_spec_data.to_dict('records'):
NrmSpecRec = {'specimen': spec, 'sample': this_sample}
if coord == 'g':
NrmSpecRec['dir_tilt_correction'] = '0'
elif coord == 't':
NrmSpecRec['dir_tilt_correction'] = '100'
else:
NrmSpecRec['dir_tilt_correction'] = '-1'
if not orient:
NrmSpecRec['dir_dec'] = m['dir_dec']
NrmSpecRec['dir_inc'] = m['dir_inc']
NrmSpecRec['method_codes'] = 'SO-NO'
NrmSpecRecs.append(NrmSpecRec)
else: # do geographic correction
# get the azimuth
or_info, az_type = pmag.get_orient(this_sample_data,
this_sample,
data_model=3)
if 'azimuth' in or_info.keys() and or_info['azimuth'] != "":
azimuth = or_info['azimuth']
dip = or_info['dip']
gdec, ginc = pmag.dogeo(m['dir_dec'], m['dir_inc'],
azimuth, dip)
if tilt:
# try tilt correction
if 'bed_dip' in or_info.keys(
) and or_info['bed_dip'] != "":
bed_dip = or_info['bed_dip']
bed_dip_dir = or_info['bed_dip_direction']
bdec, binc = pmag.dogeo(gdec, ginc, bed_dip_dir,
bed_dip)
NrmSpecRec['dir_dec'] = bdec
NrmSpecRec['dir_inc'] = binc
NrmSpecRec['method_codes'] = az_type
NrmSpecRecs.append(NrmSpecRec)
else:
print('no bedding orientation data for ', spec)
else:
NrmSpecRec['dir_dec'] = gdec
NrmSpecRec['dir_inc'] = ginc
NrmSpecRec['method_codes'] = az_type
NrmSpecRecs.append(NrmSpecRec)
else:
print('no geo orientation data for ', spec)
pmag.magic_write(out_file, NrmSpecRecs, 'specimens')
def main():
"""
NAME
nrm_specimens_magic.py
Note: this program has been deprecated and is not maintained
DESCRIPTION
converts NRM data in a measurements type file to
geographic and tilt corrected data in a specimens type file
SYNTAX
nrm_specimens_magic.py [-h][command line options]
OPTIONS:
-h prints the help message and quits
-f MFILE: specify input file
-fsa SFILE: specify samples format file [with orientations]
-F PFILE: specify output file
-A do not average replicate measurements
-crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted)
NB: you must have the SFILE in this directory
DEFAULTS
MFILE: measurements.txt
PFILE: nrm_specimens.txt
SFILE: samples.txt
coord: g
average replicate measurements?: YES
"""
#
# define some variables
#
beg, end, pole, geo, tilt, askave, save = 0, 0, [], 0, 0, 0, 0
samp_file = 1
args = sys.argv
geo, tilt, orient = 0, 0, 0
doave = 1
user, comment, doave, coord = "", "", 1, "g"
geo, orient = 1, 1
dir_path = '.'
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
meas_file = dir_path + "/measurements.txt"
spec_file = dir_path + "/specimens.txt"
samp_file = dir_path + "/samples.txt"
out_file = dir_path + "/nrm_specimens.txt"
if "-A" in args:
doave = 0
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
out_file = dir_path + '/' + sys.argv[ind + 1]
speclist = []
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + '/' + sys.argv[ind + 1]
if "-crd" in args:
ind = args.index("-crd")
coord = sys.argv[ind + 1]
if coord == "t":
tilt, orient, geo = 1, 1, 1
#
# read in data
#
meas_data = pd.read_csv(meas_file, header=1, sep='\t')
meas_data = meas_data[meas_data['method_codes'].str.contains(
'LT-NO') == True] # fish out NRM data
meas_data = meas_data[['specimen', 'dir_dec', 'dir_inc']]
meas_data = meas_data.dropna(subset=['dir_dec', 'dir_inc'])
meas_data = pd.DataFrame(meas_data)
# import samples for orientation info
#
##
if orient == 1:
spec_data = pd.read_csv(spec_file, header=1, sep='\t')
spec_data = spec_data[['specimen', 'sample']]
meas_data = pd.merge(meas_data, spec_data,
how='inner', on=['specimen'])
samp_data = pd.read_csv(samp_file, header=1, sep='\t')
#
sids = meas_data.specimen.unique() # list of specimen names
#
#
NrmSpecRecs = []
for spec in sids:
gdec, ginc, bdec, binc = "", "", "", ""
this_spec_data = meas_data[meas_data.specimen.str.contains(spec)]
this_sample = this_spec_data['sample'].iloc[-1]
this_sample_data = samp_data[samp_data['sample'].str.contains(
this_sample)]
this_sample_data = this_sample_data.to_dict('records')
for m in this_spec_data.to_dict('records'):
NrmSpecRec = {'specimen': spec, 'sample': this_sample}
if coord == 'g':
NrmSpecRec['dir_tilt_correction'] = '0'
elif coord == 't':
NrmSpecRec['dir_tilt_correction'] = '100'
else:
NrmSpecRec['dir_tilt_correction'] = '-1'
if not orient:
NrmSpecRec['dir_dec'] = m['dir_dec']
NrmSpecRec['dir_inc'] = m['dir_inc']
NrmSpecRec['method_codes'] = 'SO-NO'
NrmSpecRecs.append(NrmSpecRec)
else: # do geographic correction
# get the azimuth
or_info, az_type = pmag.get_orient(
this_sample_data, this_sample, data_model=3)
if 'azimuth' in or_info.keys() and or_info['azimuth'] != "":
azimuth = or_info['azimuth']
dip = or_info['dip']
gdec, ginc = pmag.dogeo(
m['dir_dec'], m['dir_inc'], azimuth, dip)
if tilt:
# try tilt correction
if 'bed_dip' in or_info.keys() and or_info['bed_dip'] != "":
bed_dip = or_info['bed_dip']
bed_dip_dir = or_info['bed_dip_direction']
bdec, binc = pmag.dogeo(
gdec, ginc, bed_dip_dir, bed_dip)
NrmSpecRec['dir_dec'] = bdec
NrmSpecRec['dir_inc'] = binc
NrmSpecRec['method_codes'] = az_type
NrmSpecRecs.append(NrmSpecRec)
else:
print('no bedding orientation data for ', spec)
else:
NrmSpecRec['dir_dec'] = gdec
NrmSpecRec['dir_inc'] = ginc
NrmSpecRec['method_codes'] = az_type
NrmSpecRecs.append(NrmSpecRec)
else:
print('no geo orientation data for ', spec)
pmag.magic_write(out_file, NrmSpecRecs, 'specimens')
def main():
"""
NAME
nrm_specimens_magic.py
DESCRIPTION
converts NRM data in a magic_measurements type file to
geographic and tilt corrected data in a pmag_specimens type file
SYNTAX
nrm_specimens_magic.py [-h][command line options]
OPTIONS:
-h prints the help message and quits
-f MFILE: specify input file
-fsa SFILE: specify er_samples format file [with orientations]
-F PFILE: specify output file
-A do not average replicate measurements
-crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted)
NB: you must have the SFILE in this directory
DEFAULTS
MFILE: magic_measurements.txt
PFILE: nrm_specimens.txt
SFILE: er_samples.txt
coord: specimen
average replicate measurements?: YES
"""
#
# define some variables
#
beg, end, pole, geo, tilt, askave, save = 0, 0, [], 0, 0, 0, 0
samp_file = 1
args = sys.argv
geo, tilt, orient = 0, 0, 0
doave = 1
user, comment, doave, coord = "", "", 1, ""
dir_path = "."
if "-h" in args:
print main.__doc__
sys.exit()
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
meas_file = dir_path + "/magic_measurements.txt"
pmag_file = dir_path + "/nrm_specimens.txt"
samp_file = dir_path + "/er_samples.txt"
if "-A" in args:
doave = 0
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
pmag_file = dir_path + "/" + sys.argv[ind + 1]
speclist = []
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + "/" + sys.argv[ind + 1]
if "-crd" in args:
ind = args.index("-crd")
coord = sys.argv[ind + 1]
if coord == "g":
geo, orient = 1, 1
if coord == "t":
tilt, orient, geo = 1, 1, 1
#
# read in data
if samp_file != "":
samp_data, file_type = pmag.magic_read(samp_file)
if file_type != "er_samples":
print file_type
print "This is not a valid er_samples file "
sys.exit()
else:
print samp_file, " read in with ", len(samp_data), " records"
else:
print "no orientations - will create file in specimen coordinates"
geo, tilt, orient = 0, 0, 0
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != "magic_measurements":
print file_type
print file_type, "This is not a valid magic_measurements file "
sys.exit()
#
if orient == 1:
# set orientation priorities
SO_methods = []
orientation_priorities = {
"0": "SO-SUN",
"1": "SO-GPS-DIFF",
"2": "SO-SIGHT-BACK",
"3": "SO-CMD-NORTH",
"4": "SO-MAG",
}
for rec in samp_data:
if "magic_method_codes" in rec:
methlist = rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods:
SO_methods.append(meth.strip())
#
# sort the sample names
#
sids = pmag.get_specs(meas_data)
#
#
PmagSpecRecs = []
for s in sids:
skip = 0
recnum = 0
PmagSpecRec = {}
PmagSpecRec["er_analyst_mail_names"] = user
method_codes, inst_code = [], ""
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth = []
for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record
if rec["er_specimen_name"] == s:
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
PmagSpecRec["er_citation_names"] = "This study"
PmagSpecRec["magic_instrument_codes"] = ""
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec["magic_experiment_name"]
if len(rec["magic_instrument_codes"]) > len(inst_code):
inst_code = rec["magic_instrument_codes"]
PmagSpecRec["magic_instrument_codes"] = inst_code # copy over instruments
break
#
# now check for correct method labels for all measurements
#
nrm_data = []
for meas_rec in meas_data:
if meas_rec["er_specimen_name"] == PmagSpecRec["er_specimen_name"]:
meths = meas_rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:
meas_meth.append(meth)
if "LT-NO" in meas_meth:
nrm_data.append(meas_rec)
#
data, units = pmag.find_dmag_rec(s, nrm_data)
#
datablock = data
#
# find replicate measurements at NRM step and average them
#
Specs = []
if doave == 1:
step_meth, avedata = pmag.vspec(data)
if len(avedata) != len(datablock):
method_codes.append("DE-VM")
SpecRec = avedata[0]
print "averaging data "
else:
SpecRec = data[0]
Specs.append(SpecRec)
else:
for spec in data:
Specs.append(spec)
for SpecRec in Specs:
#
# do geo or stratigraphic correction now
#
if geo == 1:
#
# find top priority orientation method
redo, p = 1, 0
if len(SO_methods) <= 1:
az_type = SO_methods[0]
orient = pmag.find_samp_rec(PmagSpecRec["er_sample_name"], samp_data, az_type)
if orient["sample_azimuth"] != "":
method_codes.append(az_type)
redo = 0
while redo == 1:
if p >= len(orientation_priorities):
print "no orientation data for ", s
skip, redo = 1, 0
break
az_type = orientation_priorities[str(p)]
orient = pmag.find_samp_rec(PmagSpecRec["er_sample_name"], samp_data, az_type)
if orient["sample_azimuth"] != "":
method_codes.append(az_type.strip())
redo = 0
elif orient["sample_azimuth"] == "":
p += 1
#
# if stratigraphic selected, get stratigraphic correction
#
if skip == 0 and orient["sample_azimuth"] != "" and orient["sample_dip"] != "":
d_geo, i_geo = pmag.dogeo(SpecRec[1], SpecRec[2], orient["sample_azimuth"], orient["sample_dip"])
SpecRec[1] = d_geo
SpecRec[2] = i_geo
if tilt == 1 and "sample_bed_dip" in orient.keys() and orient["sample_bed_dip"] != "":
d_tilt, i_tilt = pmag.dotilt(
d_geo, i_geo, orient["sample_bed_dip_direction"], orient["sample_bed_dip"]
)
SpecRec[1] = d_tilt
SpecRec[2] = i_tilt
if skip == 0:
PmagSpecRec["specimen_dec"] = "%7.1f " % (SpecRec[1])
PmagSpecRec["specimen_inc"] = "%7.1f " % (SpecRec[2])
if geo == 1 and tilt == 0:
PmagSpecRec["specimen_tilt_correction"] = "0"
if geo == 1 and tilt == 1:
PmagSpecRec["specimen_tilt_correction"] = "100"
if geo == 0 and tilt == 0:
PmagSpecRec["specimen_tilt_correction"] = "-1"
PmagSpecRec["specimen_direction_type"] = "l"
PmagSpecRec["magic_method_codes"] = "LT-NO"
if len(method_codes) != 0:
methstring = ""
for meth in method_codes:
methstring = methstring + ":" + meth
PmagSpecRec["magic_method_codes"] = methstring[1:]
PmagSpecRec["specimen_description"] = "NRM data"
PmagSpecRecs.append(PmagSpecRec)
pmag.magic_write(pmag_file, PmagSpecRecs, "pmag_specimens")
print "Data saved in ", pmag_file