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():
"""
NAME
lnp_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimen formatted file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
SYNTAX
lnp_magic [command line options]
INPUT
takes magic formatted pmag_specimens file
OUPUT
prints site_name n_lines n_planes K alpha95 dec inc R
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is 'pmag_specimens.txt'
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is specimen
-fmt [svg,png,jpg] format for plots, default is svg
-P: do not plot
-F FILE, specify output file of dec, inc, alpha95 data for plotting with plotdi_a and plotdi_e
-exc use criteria in pmag_criteria.txt
"""
dir_path='.'
FIG={} # plot dictionary
FIG['eqarea']=1 # eqarea is figure 1
in_file,plot_key,coord='pmag_specimens.txt','er_site_name',"-1"
out_file=""
fmt,plot='svg',1
Crits=""
M,N=180.,1
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 '-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 '-F' in sys.argv:
ind=sys.argv.index("-F")
out_file=sys.argv[ind+1]
out=open(dir_path+'/'+out_file,'w')
if '-crd' in sys.argv:
ind=sys.argv.index("-crd")
crd=sys.argv[ind+1]
if crd=='s':coord="-1"
if crd=='g':coord="0"
if crd=='t':coord="100"
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-P' in sys.argv:plot=0
#
in_file=dir_path+'/'+in_file
Specs,file_type=pmag.magic_read(in_file)
sitelist=[]
for rec in Specs:
if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
sitelist.sort()
if plot==1:
import pmagplotlib
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],4,4)
for site in sitelist:
print site
data=[]
for spec in Specs:
if 'specimen_tilt_correction' not in spec.keys():spec['specimen_tilt_correction']='-1' # assume unoriented
if spec['er_site_name']==site:
if 'specimen_mad' not in spec.keys() or spec['specimen_mad']=="":
if 'specimen_alpha95' in spec.keys() and spec['specimen_alpha95']!="":
spec['specimen_mad']=spec['specimen_alpha95']
else:
spec['specimen_mad']='180'
if spec['specimen_tilt_correction']==coord and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N:
rec={}
for key in spec.keys():rec[key]=spec[key]
rec["dec"]=float(spec['specimen_dec'])
rec["inc"]=float(spec['specimen_inc'])
rec["tilt_correction"]=spec['specimen_tilt_correction']
data.append(rec)
if len(data)>2:
fpars=pmag.dolnp(data,'specimen_direction_type')
print "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']))
print '% tilt correction: ',coord
if plot==1:
pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
ans=raw_input("s[a]ve plot, [q]uit, <return> to continue:\n ")
if ans=="a":
files={}
files['eqarea']=site+'_'+crd+'_'+'eqarea'+'.'+fmt
pmagplotlib.saveP(EQ,files)
if ans=="q": sys.exit()
else:
print 'skipping site - not enough data with specified coordinate system'
def main():
"""
NAME
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from zeq_specimens_g.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 zeq_specimens_s.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 = "zeq_specimens_s.txt"
sampfile = "er_samples.txt"
out_file = ""
fmt, plot = "svg", 1
Crits = ""
M, N = 180.0, 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
#
in_file = dir_path + "/" + in_file
sampfile = dir_path + "/" + sampfile
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 = []
for spec in Specs:
if spec["er_site_name"] == site:
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"
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")
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"]) - 180.0,
-float(spec["sample_dip"]),
)
XY = pmag.dimap(d, i)
pmagplotlib.plotXY(EQ["eqarea"], [XY[0]], [XY[1]], "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"]) - 180.0,
float(spec["sample_dip"]),
)
XY = pmag.dimap(d, i)
pmagplotlib.plotXY(EQ["eqarea"], [XY[0]], [XY[1]], "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, "b.", "", "", "")
pmagplotlib.plotXY(EQ["eqarea"], X_up, Y_up, "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
