def test_magic_read_success(self):
fname = os.path.join(WD, "data_files", "3_0", "McMurdo", "sites.txt")
data, ftype = pmag.magic_read(fname)
self.assertEqual(ftype, 'sites')
self.assertEqual(len(data), 542)
data, ftype, magic_keys = pmag.magic_read(fname, return_keys=True)
self.assertEqual(magic_keys[-1], 'vgp_n_samples')
def test_magic_read_success(self):
fname = os.path.join(WD, "data_files", "3_0", "McMurdo", "sites.txt")
data, ftype = pmag.magic_read(fname)
self.assertEqual(ftype, 'sites')
self.assertEqual(len(data), 542)
data, ftype, magic_keys = pmag.magic_read(fname,
return_keys=True)
self.assertEqual(magic_keys[-1], 'vgp_n_samples')
def main():
"""
NAME
measurements_normalize.py
DESCRIPTION
takes magic_measurements file and normalized moment by sample_weight and sample_volume in the er_specimens table
SYNTAX
measurements_normalize.py [command line options]
OPTIONS
-f FILE: specify input file, default is: magic_measurements.txt
-fsp FILE: specify input specimen file, default is: er_specimens.txt
-F FILE: specify output measurements, default is to overwrite input file
"""
#
# initialize variables
#
#
#
dir_path='.'
if "-WD" in sys.argv:
ind=sys.argv.index("-WD")
dir_path=sys.argv[ind+1]
meas_file,spec_file= dir_path+"/magic_measurements.txt",dir_path+"/er_specimens.txt"
out_file=meas_file
MeasRecs,SpecRecs=[],[]
OutRecs=[]
if "-h" in sys.argv:
print(main.__doc__)
sys.exit()
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")
spec_file=dir_path+'/'+sys.argv[ind+1]
if "-F" in sys.argv:
ind=sys.argv.index("-F")
out_file=dir_path+'/'+sys.argv[ind+1]
MeasRecs,file_type=pmag.magic_read(meas_file)
Specs,file_type=pmag.magic_read(spec_file)
for rec in MeasRecs:
if 'measurement_magn_moment' in list(rec.keys()) and rec['measurement_magn_moment'] != "":
for spec in Specs:
if spec['er_specimen_name']==rec['er_specimen_name']:
if 'specimen_weight' in list(spec.keys()) and spec['specimen_weight']!="":
rec['measurement_magn_mass']='%e'%(old_div(float(rec['measurement_magn_moment']),float(spec['specimen_weight'])))
if 'specimen_volume' in list(spec.keys()) and spec['specimen_volume']!="":
rec['measurement_magn_volume']='%e'%(old_div(float(rec['measurement_magn_moment']),float(spec['specimen_volume'])))
break
if 'measurement_magn_volume' not in list(rec.keys()): rec['measurement_magn_volume']=''
if 'measurement_magn_mass' not in list(rec.keys()): rec['measurement_magn_mass']=''
OutRecs.append(rec)
pmag.magic_write(out_file,OutRecs,"magic_measurements")
print("Data saved in ", out_file)
def get_Data(magic_file):
#------------------------------------------------
# Read magic measurement file and sort to blocks
#------------------------------------------------
Data = {}
try:
meas_data, file_type = pmag.magic_read(magic_file)
except:
print "-E- ERROR: Cant read magic_measurement.txt file. File is corrupted."
return Data
# get list of unique specimen names
#sids=pmag.get_specs(meas_data) # samples ID's
for rec in meas_data:
s = rec["er_specimen_name"]
method_codes = rec["magic_method_codes"].strip('\n')
method_codes.replace(" ", "")
methods = method_codes.split(":")
if "LP-AN-TRM" in methods:
if s not in Data.keys():
Data[s] = {}
if 'atrmblock' not in Data[s].keys():
Data[s]['atrmblock'] = []
Data[s]['atrmblock'].append(rec)
if "LP-AN-ARM" in methods:
if s not in Data.keys():
Data[s] = {}
if 'aarmblock' not in Data[s].keys():
Data[s]['aarmblock'] = []
Data[s]['aarmblock'].append(rec)
return (Data)
def main():
"""
NAME
change_case_magic.py
DESCRIPTION
picks out key and converts to upper or lower case
SYNTAX
change_case_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-F FILE: specify output magic format file , default is to overwrite input file
-keys KEY1:KEY2 specify colon delimited list of keys to convert
-[U,l] : specify [U]PPER or [l]ower case, default is lower
"""
dir_path = "./"
change = 'l'
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
magic_file = dir_path + '/' + sys.argv[ind + 1]
else:
print(main.__doc__)
sys.exit()
if '-F' in sys.argv:
ind = sys.argv.index('-F')
out_file = dir_path + '/' + sys.argv[ind + 1]
else:
out_file = magic_file
if '-keys' in sys.argv:
ind = sys.argv.index('-keys')
grab_keys = sys.argv[ind + 1].split(":")
else:
print(main.__doc__)
sys.exit()
if '-U' in sys.argv: change = 'U'
#
#
# get data read in
Data, file_type = pmag.magic_read(magic_file)
if len(Data) > 0:
for grab_key in grab_keys:
for rec in Data:
if change == 'l':
rec[grab_key] = rec[grab_key].lower()
else:
rec[grab_key] = rec[grab_key].upper()
else:
print('bad file name')
pmag.magic_write(out_file, Data, file_type)
def main():
"""
NAME
change_case_magic.py
DESCRIPTION
picks out key and converts to upper or lower case
SYNTAX
change_case_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-F FILE: specify output magic format file , default is to overwrite input file
-keys KEY1:KEY2 specify colon delimited list of keys to convert
-[U,l] : specify [U]PPER or [l]ower case, default is lower
"""
dir_path="./"
change='l'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
magic_file=dir_path+'/'+sys.argv[ind+1]
else:
print(main.__doc__)
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
out_file=dir_path+'/'+sys.argv[ind+1]
else: out_file=magic_file
if '-keys' in sys.argv:
ind=sys.argv.index('-keys')
grab_keys=sys.argv[ind+1].split(":")
else:
print(main.__doc__)
sys.exit()
if '-U' in sys.argv: change='U'
#
#
# get data read in
Data,file_type=pmag.magic_read(magic_file)
if len(Data)>0:
for grab_key in grab_keys:
for rec in Data:
if change=='l':
rec[grab_key]=rec[grab_key].lower()
else:
rec[grab_key]=rec[grab_key].upper()
else:
print('bad file name')
pmag.magic_write(out_file,Data,file_type)
def test_bgc_with_append(self):
options = {'input_dir_path': self.input_dir, 'mag_file': 'BC0-3A'}
program_ran, outfile = bgc_magic.convert(**options)
self.assertTrue(program_ran)
options['append'] = True
program_ran, outfile = bgc_magic.convert(**options)
self.assertTrue(program_ran)
lines, file_type = pmag.magic_read(os.path.join(WD, 'specimens.txt'))
self.assertEqual(len(lines), 2)
def test_bgc_with_append(self):
options = {'input_dir_path': self.input_dir, 'mag_file': 'BC0-3A'}
program_ran, outfile = bgc_magic.convert(**options)
self.assertTrue(program_ran)
options['append'] = True
program_ran, outfile = bgc_magic.convert(**options)
self.assertTrue(program_ran)
lines, file_type = pmag.magic_read(os.path.join(WD, 'specimens.txt'))
self.assertEqual(len(lines), 2)
def main():
"""
NAME
extract_methods.py
DESCRIPTION
reads in a magic table and creates a file with method codes
SYNTAX
extract_methods.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify magic format input file, default is magic_measurements.txt
-F FILE: specify method code output file, default is magic_methods.txt
"""
citation='This study'
args=sys.argv
outfile='magic_methods.txt'
infile='magic_measurements.txt'
#
# get command line arguments
#
dir_path='.'
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if '-F' in args:
ind=args.index("-F")
outfile=args[ind+1]
if '-f' in args:
ind=args.index("-f")
infile=args[ind+1]
infile=dir_path+'/'+infile
outfile=dir_path+'/'+outfile
data,file_type=pmag.magic_read(infile)
MethRecs=[]
methods=[]
for rec in data:
meths=rec['magic_method_codes'].split(":")
for meth in meths:
if meth not in methods:
MethRec={}
methods.append(meth)
MethRec['magic_method_code']=meth
MethRecs.append(MethRec)
pmag.magic_write(outfile,MethRecs,'magic_methods')
def main():
"""
NAME
extract_methods.py
DESCRIPTION
reads in a magic table and creates a file with method codes
SYNTAX
extract_methods.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify magic format input file, default is magic_measurements.txt
-F FILE: specify method code output file, default is magic_methods.txt
"""
citation='This study'
args=sys.argv
outfile='magic_methods.txt'
infile='magic_measurements.txt'
#
# get command line arguments
#
dir_path='.'
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-F' in args:
ind=args.index("-F")
outfile=args[ind+1]
if '-f' in args:
ind=args.index("-f")
infile=args[ind+1]
infile=dir_path+'/'+infile
outfile=dir_path+'/'+outfile
data,file_type=pmag.magic_read(infile)
MethRecs=[]
methods=[]
for rec in data:
meths=rec['magic_method_codes'].split(":")
for meth in meths:
if meth not in methods:
MethRec={}
methods.append(meth)
MethRec['magic_method_code']=meth
MethRecs.append(MethRec)
pmag.magic_write(outfile,MethRecs,'magic_methods')
def main():
"""
NAME
grab_magic_key.py
DESCRIPTION
picks out key and saves to file
SYNTAX
grab_magic_key.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-key KEY: specify key to print to standard output
"""
dir_path = "./"
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
magic_file = dir_path+'/'+sys.argv[ind+1]
else:
print(main.__doc__)
sys.exit()
if '-key' in sys.argv:
ind = sys.argv.index('-key')
grab_key = sys.argv[ind+1]
else:
print(main.__doc__)
sys.exit()
#
#
# get data read in
Data, file_type = pmag.magic_read(magic_file)
if len(Data) > 0:
for rec in Data:
print(rec[grab_key])
else:
print('bad file name')
def main():
"""
NAME
grab_magic_key.py
DESCRIPTION
picks out key and saves to file
SYNTAX
grab_magic_key.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-key KEY: specify key to print to standard output
"""
dir_path = "./"
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
magic_file = dir_path + '/' + sys.argv[ind + 1]
else:
print(main.__doc__)
sys.exit()
if '-key' in sys.argv:
ind = sys.argv.index('-key')
grab_key = sys.argv[ind + 1]
else:
print(main.__doc__)
sys.exit()
#
#
# get data read in
Data, file_type = pmag.magic_read(magic_file)
if len(Data) > 0:
for rec in Data:
print(rec[grab_key])
else:
print('bad file name')
def test_make_plots(self):
dir_path = os.path.join(WD, 'data_files', '3_0', 'Osler')
image_file = os.path.join(dir_path, 'images.txt')
os.chdir(dir_path)
for filename in glob.glob("*error*"):
os.remove(filename)
os.system("new_make_magic_plots.py")
self.assertFalse(glob.glob("errors.txt"))
self.assertTrue(os.path.exists(image_file))
lines = pmag.magic_read(image_file)[0]
self.assertEqual(len(lines), 7)
self.assertFalse("image" in lines[0].keys())
if pmagplotlib.isServer:
self.assertFalse(glob.glob("thumbnail_errors.txt"))
self.assertEqual(14, len(glob.glob("*.png")))
self.assertEqual(7, len(glob.glob("*thumb*.png")))
else:
self.assertEqual(10, len(glob.glob("*.png")))
self.assertEqual(5, len(glob.glob("*thumb*.png")))
def test_make_plots_long(self):
#if not pmagplotlib.isServer:
# # only run this annoyingly slow test 10% of the time
# num = random.randint(1, 10)
# if num != 3:
# return
# make a backup of images.txt
os.chdir(os.path.join(WD, 'data_files', '3_0', 'McMurdo'))
for filename in glob.glob("*error*"):
os.remove(filename)
os.system("new_make_magic_plots.py")
lines = pmag.magic_read("images.txt")[0]
for line in lines[-3:]:
print(line)
self.assertEqual(len(lines), 541)
self.assertFalse("image" in lines[0].keys())
self.assertFalse(glob.glob("errors.txt"))
num_pngs = len(glob.glob("*png"))
num_thumbnails = len(glob.glob("*thumb.png"))
self.assertEqual(num_pngs / 2, num_thumbnails)
self.assertFalse(glob.glob("thumbnail_errors.txt"))
def get_Data(magic_file):
#------------------------------------------------
# Read magic measurement file and sort to blocks
#------------------------------------------------
Data={}
try:
meas_data,file_type=pmag.magic_read(magic_file)
except:
print "-E- ERROR: Cant read magic_measurement.txt file. File is corrupted."
return Data
# get list of unique specimen names
#sids=pmag.get_specs(meas_data) # samples ID's
for rec in meas_data:
s=rec["er_specimen_name"]
method_codes= rec["magic_method_codes"].strip('\n')
method_codes.replace(" ","")
methods=method_codes.split(":")
if "LP-AN-TRM" in methods:
if s not in Data.keys():
Data[s]={}
if 'atrmblock' not in Data[s].keys():
Data[s]['atrmblock']=[]
Data[s]['atrmblock'].append(rec)
if "LP-AN-ARM" in methods:
if s not in Data.keys():
Data[s]={}
if 'aarmblock' not in Data[s].keys():
Data[s]['aarmblock']=[]
Data[s]['aarmblock'].append(rec)
return (Data)
def main():
"""
NAME
thellier_magic.py
DESCRIPTION
plots Thellier-Thellier, allowing interactive setting of bounds
and customizing of selection criteria. Saves and reads interpretations
from a pmag_specimen formatted table, default: thellier_specimens.txt
SYNTAX
thellier_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set magic_measurements input file
-fsp PRIOR, set pmag_specimen prior interpretations file
-fan ANIS, set rmag_anisotropy file for doing the anisotropy corrections
-fcr CRIT, set criteria file for grading.
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (default format)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds adn quits
-b BEG END: sets bounds for calculation
BEG: starting step for slope calculation
END: ending step for slope calculation
-z use only z component difference for pTRM calculation
DEFAULTS
MEAS: magic_measurements.txt
REDO: thellier_redo
CRIT: NONE
PRIOR: NONE
OUTPUT
figures:
ALL: numbers refer to temperature steps in command line window
1) Arai plot: closed circles are zero-field first/infield
open circles are infield first/zero-field
triangles are pTRM checks
squares are pTRM tail checks
VDS is vector difference sum
diamonds are bounds for interpretation
2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes
X rotated to NRM direction
3) (De/Re)Magnetization diagram:
circles are NRM remaining
squares are pTRM gained
4) equal area projections:
green triangles are pTRM gained direction
red (purple) circles are lower(upper) hemisphere of ZI step directions
blue (cyan) squares are lower(upper) hemisphere IZ step directions
5) Optional: TRM acquisition
6) Optional: TDS normalization
command line window:
list is: temperature step numbers, temperatures (C), Dec, Inc, Int (units of magic_measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates .svg format files with specimen_name, plot type as name
"""
#
# initializations
#
meas_file,critout,inspec="magic_measurements.txt","","thellier_specimens.txt"
first=1
inlt=0
version_num=pmag.get_version()
TDinit,Tinit,field,first_save=0,0,-1,1
user,comment,AniSpec,locname="",'',"",""
ans,specimen,recnum,start,end=0,0,0,0,0
plots,pmag_out,samp_file,style=0,"","","svg"
verbose=pmagplotlib.verbose
fmt='.'+style
#
# default acceptance criteria
#
accept=pmag.default_criteria(0)[0] # set the default criteria
#
# parse command line options
#
Zdiff,anis=0,0
spc,BEG,END="","",""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
inspec=sys.argv[ind+1]
if '-fan' in sys.argv:
ind=sys.argv.index('-fan')
anisfile=sys.argv[ind+1]
anis=1
anis_data,file_type=pmag.magic_read(anisfile)
if verbose: print "Anisotropy data read in from ", anisfile
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-dpi' in sys.argv:
ind=sys.argv.index('-dpi')
dpi='.'+sys.argv[ind+1]
else: dpi=100
if '-sav' in sys.argv:
plots=1
verbose=0
if '-z' in sys.argv: Zdiff=1
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
spc=sys.argv[ind+1]
if '-b' in sys.argv:
ind=sys.argv.index('-b')
BEG=int(sys.argv[ind+1])
END=int(sys.argv[ind+2])
if '-fcr' in sys.argv:
ind=sys.argv.index('-fcr')
critout=sys.argv[ind+1]
crit_data,file_type=pmag.magic_read(critout)
if file_type!='pmag_criteria':
if verbose: print 'bad pmag_criteria file, using no acceptance criteria'
accept=pmag.default_criteria(1)[0]
else:
if verbose: print "Acceptance criteria read in from ", critout
accept={'pmag_criteria_code':'ACCEPTANCE','er_citation_names':'This study'}
for critrec in crit_data:
if 'sample_int_sigma_uT' in critrec.keys(): # accommodate Shaar's new criterion
critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key]!='':
accept[key]=critrec[key]
try:
open(inspec,'rU')
PriorRecs,file_type=pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print file_type
print file_type,inspec," is not a valid pmag_specimens file "
sys.exit()
for rec in PriorRecs:
if 'magic_software_packages' not in rec.keys():rec['magic_software_packages']=""
except IOError:
PriorRecs=[]
if verbose:print "starting new specimen interpretation file: ",inspec
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()
backup=0
# define figure numbers for arai, zijderveld and
# de-,re-magization diagrams
AZD={}
AZD['deremag'], AZD['zijd'],AZD['arai'],AZD['eqarea']=1,2,3,4
pmagplotlib.plot_init(AZD['arai'],5,5)
pmagplotlib.plot_init(AZD['zijd'],5,5)
pmagplotlib.plot_init(AZD['deremag'],5,5)
pmagplotlib.plot_init(AZD['eqarea'],5,5)
#
#
#
# get list of unique specimen names
#
CurrRec=[]
sids=pmag.get_specs(meas_data)
# get plots for specimen s - default is just to step through arai diagrams
#
if spc!="": specimen =sids.index(spc)
while specimen < len(sids):
methcodes=[]
if verbose:
print sids[specimen],specimen+1, 'of ', len(sids)
MeasRecs=[]
s=sids[specimen]
datablock,trmblock,tdsrecs=[],[],[]
PmagSpecRec={}
if first==0:
for key in keys:PmagSpecRec[key]="" # make sure all new records have same set of keys
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["specimen_correction"]='u'
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"]==s:
MeasRecs.append(rec)
if "magic_method_codes" not in rec.keys():
rec["magic_method_codes"]=""
methods=rec["magic_method_codes"].split(":")
meths=[]
for meth in methods:
meths.append(meth.strip()) # take off annoying spaces
methods=""
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
methods=methods+meth+":"
methods=methods[:-1]
rec["magic_method_codes"]=methods
if "LP-PI-TRM" in meths: datablock.append(rec)
if "LP-TRM" in meths: trmblock.append(rec)
if "LP-TRM-TD" in meths: tdsrecs.append(rec)
if len(trmblock)>2 and inspec!="":
if Tinit==0:
Tinit=1
AZD['TRM']=5
pmagplotlib.plot_init(AZD['TRM'],5,5)
elif Tinit==1: # clear the TRM figure if not needed
pmagplotlib.clearFIG(AZD['TRM'])
if len(tdsrecs)>2:
if TDinit==0:
TDinit=1
AZD['TDS']=6
pmagplotlib.plot_init(AZD['TDS'],5,5)
elif TDinit==1: # clear the TDS figure if not needed
pmagplotlib.clearFIG(AZD['TDS'])
if len(datablock) <4:
if backup==0:
specimen+=1
if verbose:
print 'skipping specimen - moving forward ', s
else:
specimen-=1
if verbose:
print 'skipping specimen - moving backward ', s
#
# collect info for the PmagSpecRec dictionary
#
else:
rec=datablock[0]
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'].replace('/','-')
if "er_expedition_name" in rec.keys():PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():rec["magic_instrument_codes"]=""
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
PmagSpecRec["measurement_step_unit"]="K"
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
meths=rec["magic_method_codes"].split()
# sort data into types
araiblock,field=pmag.sortarai(datablock,s,Zdiff)
first_Z=araiblock[0]
GammaChecks=araiblock[5]
if len(first_Z)<3:
if backup==0:
specimen+=1
if verbose:
print 'skipping specimen - moving forward ', s
else:
specimen-=1
if verbose:
print 'skipping specimen - moving backward ', s
else:
backup=0
zijdblock,units=pmag.find_dmag_rec(s,meas_data)
recnum=0
if verbose:
print "index step Dec Inc Int Gamma"
for plotrec in zijdblock:
if GammaChecks!="":
gamma=""
for g in GammaChecks:
if g[0]==plotrec[0]-273:
gamma=g[1]
break
if gamma!="":
print '%i %i %7.1f %7.1f %8.3e %7.1f' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3],gamma)
else:
print '%i %i %7.1f %7.1f %8.3e ' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3])
recnum += 1
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
if verbose:pmagplotlib.drawFIGS(AZD)
if len(tdsrecs)>2: # a TDS experiment
tdsblock=[] # make a list for the TDS data
Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measuruement_magn_mass']
mkey,k="",0
while mkey=="" and k<len(Mkeys)-1: # find which type of intensity
key= Mkeys[k]
if key in tdsrecs[0].keys() and tdsrecs[0][key]!="": mkey=key
k+=1
if mkey=="":break # get outta here
Tnorm=""
for tdrec in tdsrecs:
meths=tdrec['magic_method_codes'].split(":")
for meth in meths: meth.replace(" ","") # strip off potential nasty spaces
if 'LT-T-I' in meths and Tnorm=="": # found first total TRM
Tnorm=float(tdrec[mkey]) # normalize by total TRM
tdsblock.append([273,zijdblock[0][3]/Tnorm,1.]) # put in the zero step
if 'LT-T-Z' in meths and Tnorm!="": # found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock
step=float(tdrec['treatment_temp'])
Tint=""
if mkey!="":
Tint=float(tdrec[mkey])
if Tint!="":
for zrec in zijdblock:
if zrec[0]==step: # found matching
tdsblock.append([step,zrec[3]/Tnorm,Tint/Tnorm])
break
if len(tdsblock)>2:
pmagplotlib.plotTDS(AZD['TDS'],tdsblock,s+':LP-PI-TDS:')
if verbose:pmagplotlib(drawFIGS(AZD))
else:
print "Something wrong here"
if anis==1: # look up anisotropy data for this specimen
AniSpec=""
for aspec in anis_data:
if aspec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpec=aspec
if verbose: print 'Found anisotropy record...'
break
if inspec !="":
if verbose: print 'Looking up saved interpretation....'
found = 0
for k in range(len(PriorRecs)):
try:
if PriorRecs[k]["er_specimen_name"]==s:
found =1
CurrRec.append(PriorRecs[k])
for j in range(len(zijdblock)):
if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_min"]):start=j
if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_max"]):end=j
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept)
pars['measurement_step_unit']="K"
pars['experiment_type']='LP-PI-TRM'
del PriorRecs[k] # put in CurrRec, take out of PriorRecs
if errcode!=1:
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
if verbose:
print 'Saved interpretation: '
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
PmagSpecRec['specimen_int']=NLpars['banc']
if verbose:
print 'Banc= ',float(NLpars['banc'])*1e6
pmagplotlib.drawFIGS(AZD)
mpars=pmag.domean(araiblock[1],start,end,'DE-BFL')
if verbose:
print 'pTRM direction= ','%7.1f'%(mpars['specimen_dec']),' %7.1f'%(mpars['specimen_inc']),' MAD:','%7.1f'%(mpars['specimen_mad'])
if AniSpec!="":
CpTRM=pmag.Dir_anis_corr([mpars['specimen_dec'],mpars['specimen_inc']],AniSpec)
AniSpecRec=pmag.doaniscorr(PmagSpecRec,AniSpec)
if verbose:
print 'Anisotropy corrected TRM direction= ','%7.1f'%(CpTRM[0]),' %7.1f'%(CpTRM[1])
print 'Anisotropy corrected intensity= ',float(AniSpecRec['specimen_int'])*1e6
else:
print 'error on specimen ',s
except:
pass
if verbose and found==0: print ' None found :( '
if spc!="":
if BEG!="":
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,BEG,END,accept)
pars['measurement_step_unit']="K"
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
pars['specimen_grade']='' # ungraded
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
if inlt==0:
inlt=1
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files,dpi=dpi)
sys.exit()
if verbose:
ans='b'
while ans != "":
print """
s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
"""
ans=raw_input('Return for next specimen \n')
if ans=="":
specimen +=1
if ans=="d":
save_redo(PriorRecs,inspec)
CurrRec=[]
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
if verbose:pmagplotlib.drawFIGS(AZD)
if ans=='a':
files={}
for key in AZD.keys():
files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+fmt
pmagplotlib.saveP(AZD,files)
ans=""
if ans=='q':
print "Good bye"
sys.exit()
if ans=='p':
specimen =specimen -1
backup = 1
ans=""
if ans=='s':
keepon=1
spec=raw_input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
specimen =sids.index(spec)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if spec in sids[qq]:tmplist.append(sids[qq])
print specimen," not found, but this was: "
print tmplist
spec=raw_input('Select one or try again\n ')
ans=""
if ans=='b':
if end==0 or end >=len(zijdblock):end=len(zijdblock)-1
GoOn=0
while GoOn==0:
answer=raw_input('Enter index of first point for calculation: ['+str(start)+'] ')
try:
start=int(answer)
answer=raw_input('Enter index of last point for calculation: ['+str(end)+'] ')
end=int(answer)
if start >=0 and start <len(zijdblock)-2 and end >0 and end <len(zijdblock) or start>=end:
GoOn=1
else:
print "Bad endpoints - try again! "
start,end=0,len(zijdblock)
except ValueError:
print "Bad endpoints - try again! "
start,end=0,len(zijdblock)
s=sids[specimen]
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept)
pars['measurement_step_unit']="K"
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',0)
PmagSpecRec['specimen_scat']=pars['specimen_scat']
PmagSpecRec['specimen_frac']='%5.3f'%(pars['specimen_frac'])
PmagSpecRec['specimen_gmax']='%5.3f'%(pars['specimen_gmax'])
PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
PmagSpecRec["measurement_step_unit"]="K"
PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
PmagSpecRec["specimen_grade"]=pars["specimen_grade"]
if pars["method_codes"]!="":
tmpcodes=pars["method_codes"].split(":")
for t in tmpcodes:
if t.strip() not in methcodes:methcodes.append(t.strip())
PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["direction_type"]='l' # this is redundant, but helpful - won't be imported
PmagSpecRec["specimen_int_dang"]='%7.1f '%(pars["specimen_int_dang"])
PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
PmagSpecRec["specimen_drat"]='%7.1f '%(pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:methcodes.append("IE-TT")
methods=""
for meth in methcodes:
methods=methods+meth+":"
PmagSpecRec["magic_method_codes"]=methods[:-1]
PmagSpecRec["specimen_description"]=comment
PmagSpecRec["magic_software_packages"]=version_num
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
if verbose:
print 'Non-linear TRM corrected intensity= ',float(NLpars['banc'])*1e6
if verbose:pmagplotlib.drawFIGS(AZD)
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
saveit=raw_input("Save this interpretation? [y]/n \n")
if saveit!='n':
PriorRecs.append(PmagSpecRec) # put back an interpretation
specimen+=1
save_redo(PriorRecs,inspec)
ans=""
elif plots==1:
specimen+=1
if fmt != ".pmag":
files={}
for key in AZD.keys():
files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+'_'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['deremag']='DeReMag Plot'
titles['zijd']='Zijderveld Plot'
titles['arai']='Arai Plot'
AZD = pmagplotlib.addBorders(AZD,titles,black,purple)
pmagplotlib.saveP(AZD,files,dpi=dpi)
# pmagplotlib.combineFigs(s,files,3)
else: # save in pmag format
script="grep "+s+" output.mag | thellier -mfsi"
script=script+' %8.4e'%(field)
min='%i'%((pars["measurement_step_min"]-273))
Max='%i'%((pars["measurement_step_max"]-273))
script=script+" "+min+" "+Max
script=script+" |plotxy;cat mypost >>thellier.ps\n"
pltf.write(script)
pmag.domagicmag(outf,MeasRecs)
if len(CurrRec)>0:
for rec in CurrRec:
PriorRecs.append(rec)
CurrRec=[]
if plots!=1 and verbose:
ans=raw_input(" Save last plot? 1/[0] ")
if ans=="1":
if fmt != ".pmag":
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files,dpi=dpi)
else:
print "\n Good bye\n"
sys.exit()
if len(CurrRec)>0:PriorRecs.append(CurrRec) # put back an interpretation
if len(PriorRecs)>0:
save_redo(PriorRecs,inspec)
print 'Updated interpretations saved in ',inspec
if verbose:
print "Good bye"
def main():
"""
NAME
s_magic.py
DESCRIPTION
converts .s format data to magic_measurements format.
SYNTAX
s_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f SFILE specifies the .s file name
-sig last column has sigma
-typ Anisotropy type: AMS,AARM,ATRM (default is AMS)
-F RFILE specifies the rmag_anisotropy file name
-usr USER specify username
-loc location specify location/study name
-spc NUM : specify number of characters to
designate a specimen, default = 0
-spn SPECNAME, this specimen has the name SPECNAME
-n first column has specimen name
-crd [s,g,t], specify coordinate system of data
s=specimen,g=geographic,t=tilt adjusted, default is 's'
-ncn NCON: naming conventionconvention NCON
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] sample, site, location info in er_samples.txt -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
DEFAULT
RFILE: rmag_anisotropy.txt
INPUT
X11,X22,X33,X12,X23,X13 (.s format file)
X11,X22,X33,X12,X23,X13,sigma (.s format file with -sig option)
SID, X11,X22,X33,X12,X23,X13 (.s format file with -n option)
OUTPUT
rmag_anisotropy.txt format file
NOTE
because .s files do not have specimen names or location information, the output MagIC files
will have to be changed prior to importing to data base.
"""
sfile, anisfile = "", "rmag_anisotropy.txt"
location = 'unknown'
user = ""
sitename, specnum = 'unknown', 0
samp_con, Z = "", 1
user = ""
dir_path = '.'
name, sigma, spec = 0, 0, 'unknown'
type = 'AMS'
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if "-spc" in sys.argv:
ind = sys.argv.index("-spc")
specnum = int(sys.argv[ind + 1])
if specnum != 0: specnum = -specnum
if "-spn" in sys.argv:
ind = sys.argv.index("-spn")
spec = sys.argv[ind + 1]
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sfile = sys.argv[ind + 1]
if '-sig' in sys.argv: sigma = 1
if '-typ' in sys.argv:
ind = sys.argv.index('-typ')
type = sys.argv[ind + 1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
anisfile = sys.argv[ind + 1]
if '-usr' in sys.argv:
ind = sys.argv.index('-usr')
user = sys.argv[ind + 1]
if '-loc' in sys.argv:
ind = sys.argv.index('-loc')
location = sys.argv[ind + 1]
if "-n" in sys.argv:
name = 1
coord = '-1'
if "-crd" in sys.argv:
ind = sys.argv.index("-crd")
coord = sys.argv[ind + 1]
if coord == 's': coord = '-1'
if coord == 'g': coord = '0'
if coord == 't': coord = '100'
if "-ncn" in sys.argv:
ind = sys.argv.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if samp_con == '6':
Samps, filetype = pmag.magic_read(dirpath + '/er_samples.txt')
#
# get down to bidness
sfile = dir_path + '/' + sfile
anisfile = dir_path + '/' + anisfile
input = open(sfile, 'r')
AnisRecs = []
linecnt = 0
citation = "This study"
# read in data
for line in input.readlines():
AnisRec = {}
rec = line.split()
if name == 1:
k = 1
spec = rec[0]
else:
k = 0
trace = float(rec[k]) + float(rec[k + 1]) + float(rec[k + 2])
s1 = '%10.9e' % (old_div(float(rec[k]), trace))
s2 = '%10.9e' % (old_div(float(rec[k + 1]), trace))
s3 = '%10.9e' % (old_div(float(rec[k + 2]), trace))
s4 = '%10.9e' % (old_div(float(rec[k + 3]), trace))
s5 = '%10.9e' % (old_div(float(rec[k + 4]), trace))
s6 = '%10.9e' % (old_div(float(rec[k + 5]), trace))
AnisRec["er_citation_names"] = citation
AnisRec["er_specimen_name"] = spec
if specnum != 0:
AnisRec["er_sample_name"] = spec[:specnum]
else:
AnisRec["er_sample_name"] = spec
if samp_con == "6":
for samp in Samps:
if samp['er_sample_name'] == AnisRec["er_sample_name"]:
sitename = samp['er_site_name']
location = samp['er_location_name']
elif samp_con != "":
sitename = pmag.parse_site(AnisRec['er_sample_name'], samp_con, Z)
AnisRec["er_location_name"] = location
AnisRec["er_site_name"] = sitename
AnisRec["er_anylist_mail_names"] = user
if type == 'AMS':
AnisRec["anisotropy_type"] = "AMS"
AnisRec["magic_experiment_names"] = spec + ":LP-X"
else:
AnisRec["anisotropy_type"] = type
AnisRec["magic_experiment_names"] = spec + ":LP-" + type
AnisRec["anisotropy_s1"] = s1
AnisRec["anisotropy_s2"] = s2
AnisRec["anisotropy_s3"] = s3
AnisRec["anisotropy_s4"] = s4
AnisRec["anisotropy_s5"] = s5
AnisRec["anisotropy_s6"] = s6
if sigma == 1:
AnisRec["anisotropy_sigma"] = '%10.8e' % (old_div(
float(rec[k + 6]), trace))
AnisRec["anisotropy_unit"] = 'SI'
AnisRec["anisotropy_tilt_correction"] = coord
AnisRec["magic_method_codes"] = 'LP-' + type
AnisRecs.append(AnisRec)
pmag.magic_write(anisfile, AnisRecs, 'rmag_anisotropy')
print('data saved in ', anisfile)
def main():
"""
NAME
agm_magic.py
DESCRIPTION
converts Micromag agm files to magic format
SYNTAX
agm_magic.py [-h] [command line options]
OPTIONS
-usr USER: identify user, default is "" - put in quotation marks!
-bak: this is a IRM backfield curve
-f FILE, specify input file, required
-fsa SAMPFILE, specify er_samples.txt file relating samples, site and locations names,default is none
-F MFILE, specify magic measurements formatted output file, default is agm_measurements.txt
-spn SPEC, specimen name, default is base of input file name, e.g. SPECNAME.agm
-spc NUM, specify number of characters to designate a specimen, default = 0
-Fsp SPECFILE : name of er_specimens.txt file for appending data to
[default: er_specimens.txt]
-ncn NCON,: specify naming convention: default is #1 below
-syn SYN, synthetic specimen name
-loc LOCNAME : specify location/study name,
should have either LOCNAME or SAMPFILE (unless synthetic)
-ins INST : specify which instrument was used (e.g, SIO-Maud), default is ""
-u units: [cgs,SI], default is cgs
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
[8] specimen is a synthetic - it has no sample, site, location information
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
MagIC format files: magic_measurements, er_specimens, er_sample, er_site
"""
citation='This study'
MeasRecs=[]
units='cgs'
meth="LP-HYS"
version_num=pmag.get_version()
args=sys.argv
fmt='old'
er_sample_name,er_site_name,er_location_name="","",""
inst=""
er_location_name="unknown"
er_synthetic_name=""
user=""
er_site_name=""
dir_path='.'
dm=3
if "-WD" in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-ID" in args:
ind = args.index("-ID")
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
specfile = output_dir_path+'/er_specimens.txt'
output = output_dir_path+"/agm_measurements.txt"
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-bak" in args:
meth="LP-IRM-DCD"
output = output_dir_path+"/irm_measurements.txt"
if "-new" in args: fmt='new'
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
output = output_dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
agm_file= input_dir_path+'/'+args[ind+1]
er_specimen_name=args[ind+1].split('.')[0]
else:
print("agm_file field is required option")
print(main.__doc__)
sys.exit()
if '-Fsp' in args:
ind=args.index("-Fsp")
specfile= output_dir_path+'/'+args[ind+1]
specnum,samp_con,Z=0,'1',1
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-spn" in args:
ind=args.index("-spn")
er_specimen_name=args[ind+1]
#elif "-syn" not in args:
# print "you must specify a specimen name"
# sys.exit()
if "-syn" in args:
ind=args.index("-syn")
er_synthetic_name=args[ind+1]
er_specimen_name=""
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
sampfile = input_dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(sampfile)
print('sample_file successfully read in')
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-u" in args:
ind=args.index("-u")
units=args[ind+1]
dm = pmag.get_named_arg_from_sys("-DM", 2)
ErSpecRecs,filetype=pmag.magic_read(specfile)
ErSpecRec,MeasRec={},{}
ErSpecRec['er_citation_names']="This study"
ErSpecRec['er_specimen_name']=er_specimen_name
ErSpecRec['er_synthetic_name']=er_synthetic_name
if specnum!=0:
ErSpecRec["er_sample_name"]=er_specimen_name[:specnum]
else:
ErSpecRec["er_sample_name"]=er_specimen_name
if "-fsa" in args and er_synthetic_name=="":
for samp in Samps:
if samp["er_sample_name"] == ErSpecRec["er_sample_name"]:
ErSpecRec["er_location_name"]=samp["er_location_name"]
ErSpecRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6 and int(samp_con)!=8:
site=pmag.parse_site(ErSpecRec['er_sample_name'],samp_con,Z)
ErSpecRec["er_site_name"]=site
ErSpecRec["er_location_name"]=er_location_name
ErSpecRec['er_scientist_mail_names']=user.strip()
insert=1
for rec in ErSpecRecs:
if rec['er_specimen_name']==er_specimen_name:
insert=0
break
if insert==1:
ErSpecRecs.append(ErSpecRec)
ErSpecRecs,keylist=pmag.fillkeys(ErSpecRecs)
pmag.magic_write(specfile,ErSpecRecs,'er_specimens')
print("specimen name put in ",specfile)
f=open(agm_file,'r')
Data=f.readlines()
if "ASCII" not in Data[0]:fmt='new'
measnum,start=1,""
if fmt=='new': # new Micromag formatted file
end=2
for skip in range(len(Data)):
line=Data[skip]
rec=line.split()
if 'Units' in line:units=rec[-1]
if "Raw" in rec:
start=skip+2
if "Field" in rec and "Moment" in rec and start=="":
start=skip+2
break
else:
start = 2
end=1
for i in range(start,len(Data)-end): # skip header stuff
MeasRec={}
for key in list(ErSpecRec.keys()):
MeasRec[key]=ErSpecRec[key]
MeasRec['magic_instrument_codes']=inst
MeasRec['magic_method_codes']=meth
if 'er_synthetic_name' in list(MeasRec.keys()) and MeasRec['er_synthetic_name']!="":
MeasRec['magic_experiment_name']=er_synthetic_name+':'+meth
else:
MeasRec['magic_experiment_name']=er_specimen_name+':'+meth
line=Data[i]
rec=line.split(',') # data comma delimited
if rec[0]!='\n':
if units=='cgs':
field =float(rec[0])*1e-4 # convert from oe to tesla
else:
field =float(rec[0]) # field in tesla
if meth=="LP-HYS":
MeasRec['measurement_lab_field_dc']='%10.3e'%(field)
MeasRec['treatment_dc_field']=''
else:
MeasRec['measurement_lab_field_dc']=''
MeasRec['treatment_dc_field']='%10.3e'%(field)
if units=='cgs':
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])*1e-3) # convert from emu to Am^2
else:
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])) # Am^2
MeasRec['treatment_temp']='273' # temp in kelvin
MeasRec['measurement_temp']='273' # temp in kelvin
MeasRec['measurement_flag']='g'
MeasRec['measurement_standard']='u'
MeasRec['measurement_number']='%i'%(measnum)
measnum+=1
MeasRec['magic_software_packages']=version_num
MeasRecs.append(MeasRec)
# now we have to relabel LP-HYS method codes. initial loop is LP-IMT, minor loops are LP-M - do this in measurements_methods function
if meth=='LP-HYS':
recnum=0
while float(MeasRecs[recnum]['measurement_lab_field_dc'])<float(MeasRecs[recnum+1]['measurement_lab_field_dc']) and recnum+1<len(MeasRecs): # this is LP-IMAG
MeasRecs[recnum]['magic_method_codes']='LP-IMAG'
MeasRecs[recnum]['magic_experiment_name']=MeasRecs[recnum]['er_specimen_name']+":"+'LP-IMAG'
recnum+=1
#
if int(dm)==2:
pmag.magic_write(output,MeasRecs,'magic_measurements')
else:
print ('MagIC 3 is not supported yet')
sys.exit()
pmag.magic_write(output,MeasRecs,'measurements')
print("results put in ", output)
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
PLT = 1
plots = 0
user, meas_file = "", "magic_measurements.txt"
pltspec = ""
dir_path = '.'
fmt = 'png'
verbose = pmagplotlib.verbose
version_num = pmag.get_version()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind+1]
if '-f' in args:
ind = args.index("-f")
meas_file = args[ind+1]
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind+1]
verbose = 0
plots = 1
if '-fmt' in args:
ind = args.index("-fmt")
fmt = args[ind+1]
meas_file = dir_path+'/'+meas_file
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(main.__doc__)
print('bad file')
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs, RemRecs = [], []
HDD = {}
HDD['hyst'] = 1
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
#
# get list of unique experiment names and specimen names
#
experiment_names, sids = [], []
hyst_data = pmag.get_dictitem(
meas_data, 'magic_method_codes', 'LP-HYS', 'has') # get all hysteresis data
for rec in hyst_data:
if 'er_synthetic_name' in rec.keys() and rec['er_synthetic_name'] != "":
rec['er_specimen_name'] = rec['er_synthetic_name']
if rec['magic_experiment_name'] not in experiment_names:
experiment_names.append(rec['magic_experiment_name'])
if rec['er_specimen_name'] not in sids:
sids.append(rec['er_specimen_name'])
if 'measurement_temp' not in rec.keys():
# assume room T measurement unless otherwise specified
rec['measurement_temp'] = '300'
#
k = 0
if pltspec != "":
k = sids.index(pltspec)
intlist = ['measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass']
while k < len(sids):
locname, site, sample, synth = '', '', '', ''
s = sids[k]
hmeths = []
if verbose:
print(s, k+1, 'out of ', len(sids))
#
#
B, M = [], [] # B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
# get all measurements for this specimen
spec = pmag.get_dictitem(hyst_data, 'er_specimen_name', s, 'T')
if 'er_location_name' in spec[0].keys():
locname = spec[0]['er_location_name']
if 'er_site_name' in spec[0].keys():
site = spec[0]['er_site_name']
if 'er_sample_name' in spec[0].keys():
sample = spec[0]['er_sample_name']
if 'er_synthetic_name' in spec[0].keys():
synth = spec[0]['er_synthetic_name']
for m in intlist:
# get all non-blank data for this specimen
meas_data = pmag.get_dictitem(spec, m, '', 'F')
if len(meas_data) > 0:
break
c = ['k-', 'b-', 'c-', 'g-', 'm-', 'r-', 'y-']
cnum = 0
if len(meas_data) > 0:
Temps = []
xlab, ylab, title = '', '', ''
for rec in meas_data:
if rec['measurement_temp'] not in Temps:
Temps.append(rec['measurement_temp'])
for t in Temps:
print('working on t: ', t)
t_data = pmag.get_dictitem(
meas_data, 'measurement_temp', t, 'T')
B, M = [], []
for rec in t_data:
B.append(float(rec['measurement_lab_field_dc']))
M.append(float(rec[m]))
# now plot the hysteresis curve(s)
#
if len(B) > 0:
B = numpy.array(B)
M = numpy.array(M)
if t == Temps[-1]:
xlab = 'Field (T)'
ylab = m
title = 'Hysteresis: '+s
if t == Temps[0]:
pmagplotlib.clearFIG(HDD['hyst'])
pmagplotlib.plot_xy(
HDD['hyst'], B, M, sym=c[cnum], xlab=xlab, ylab=ylab, title=title)
pmagplotlib.plot_xy(HDD['hyst'], [
1.1*B.min(), 1.1*B.max()], [0, 0], sym='k-', xlab=xlab, ylab=ylab, title=title)
pmagplotlib.plot_xy(HDD['hyst'], [0, 0], [
1.1*M.min(), 1.1*M.max()], sym='k-', xlab=xlab, ylab=ylab, title=title)
if verbose:
pmagplotlib.draw_figs(HDD)
cnum += 1
if cnum == len(c):
cnum = 0
#
files = {}
if plots:
if pltspec != "":
s = pltspec
files = {}
for key in HDD.keys():
if pmagplotlib.isServer: # use server plot naming convention
if synth == '':
filename = "LO:_"+locname+'_SI:_'+site + \
'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else:
filename = 'SY:_'+synth+'_TY:_'+key+'_.'+fmt
files[key] = filename
else: # use more readable plot naming convention
if synth == '':
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
else:
filename = synth+'_'+key+'.fmt'
files[key] = filename
pmagplotlib.save_plots(HDD, files)
if pltspec != "":
sys.exit()
if verbose:
pmagplotlib.draw_figs(HDD)
ans = raw_input(
"S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans == "a":
files = {}
for key in HDD.keys():
if pmagplotlib.isServer:
print('server')
files[key] = "LO:_"+locname+'_SI:_'+site + \
'_SA:_'+sample+'_SP:_'+s+'_TY:_'+key+'_.'+fmt
else:
print('not server')
filename = ''
for item in [locname, site, sample, s, key]:
if item:
item = item.replace(' ', '_')
filename += item + '_'
if filename.endswith('_'):
filename = filename[:-1]
filename += ".{}".format(fmt)
files[key] = filename
print('files', files)
pmagplotlib.save_plots(HDD, files)
if ans == '':
k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 's':
keepon = 1
specimen = raw_input(
'Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]:
tmplist.append(sids[qq])
print(specimen, " not found, but this was: ")
print(tmplist)
specimen = raw_input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0:
if verbose:
print('skipping this one - no hysteresis data')
k += 1
def main():
"""
NAME
trmaq_magic.py
DESCTIPTION
does non-linear trm acquisisiton correction
SYNTAX
trmaq_magic.py [-h][-i][command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-f MFILE, sets magic_measurements input file
-ft TSPEC, sets thellier_specimens input file
-F OUT, sets output for non-linear TRM acquisition corrected data
DEFAULTS
MFILE: trmaq_measurements.txt
TSPEC: thellier_specimens.txt
OUT: NLT_specimens.txt
"""
meas_file = 'trmaq_measurements.txt'
tspec = "thellier_specimens.txt"
output = 'NLT_specimens.txt'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-i' in sys.argv:
meas_file = input(
"Input magic_measurements file name? [trmaq_measurements.txt] ")
if meas_file == "": meas_file = "trmaq_measurements.txt"
tspec = input(
" thellier_specimens file name? [thellier_specimens.txt] ")
if tspec == "": tspec = "thellier_specimens.txt"
output = input(
"File for non-linear TRM adjusted specimen data: [NLTspecimens.txt] "
)
if output == "": output = "NLT_specimens.txt"
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind + 1]
if '-ft' in sys.argv:
ind = sys.argv.index('-ft')
tspec = sys.argv[ind + 1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
output = sys.argv[ind + 1]
#
PLT = {'aq': 1}
pmagplotlib.plot_init(PLT['aq'], 5, 5)
#
# get name of file from command line
#
comment = ""
#
#
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()
sids = pmag.get_specs(meas_data)
specimen = 0
#
# read in thellier_specimen data
#
nrm, file_type = pmag.magic_read(tspec)
PmagSpecRecs = []
while specimen < len(sids):
#
# find corresoponding paleointensity data for this specimen
#
s = sids[specimen]
blab, best = "", ""
for nrec in nrm: # pick out the Banc data for this spec
if nrec["er_specimen_name"] == s:
blab = float(nrec["specimen_lab_field_dc"])
best = float(nrec["specimen_int"])
TrmRec = nrec
break
if blab == "":
print("skipping ", s, " : no best ")
specimen += 1
else:
print(sids[specimen], specimen + 1, 'of ', len(sids), 'Best = ',
best * 1e6)
MeasRecs = []
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"] == s:
meths = rec["magic_method_codes"].split(":")
methcodes = []
for meth in meths:
methcodes.append(meth.strip())
if "LP-TRM" in methcodes: MeasRecs.append(rec)
if len(MeasRecs) < 2:
specimen += 1
print('skipping specimen - no trm acquisition data ', s)
#
# collect info for the PmagSpecRec dictionary
#
else:
TRMs, Bs = [], []
for rec in MeasRecs:
Bs.append(float(rec['treatment_dc_field']))
TRMs.append(float(rec['measurement_magn_moment']))
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(PLT['aq'], Bs, TRMs, Bp, Mp, NLpars,
rec['magic_experiment_name'])
pmagplotlib.drawFIGS(PLT)
print('Banc= ', float(NLpars['banc']) * 1e6)
trmTC = {}
for key in list(TrmRec.keys()):
trmTC[key] = TrmRec[
key] # copy of info from thellier_specimens record
trmTC['specimen_int'] = '%8.3e' % (NLpars['banc'])
trmTC['magic_method_codes'] = TrmRec[
"magic_method_codes"] + ":DA-NL"
PmagSpecRecs.append(trmTC)
ans = input("Return for next specimen, s[a]ve plot ")
if ans == 'a':
Name = {'aq': rec['er_specimen_name'] + '_TRM.svg'}
pmagplotlib.saveP(PLT, Name)
specimen += 1
pmag.magic_write(output, PmagSpecRecs, 'pmag_specimens')
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# reset log files
for fname in ['log.txt', 'errors.txt']:
f = os.path.join(os.getcwd(), fname)
if os.path.exists(f):
os.remove(f)
dirlist = ['./']
dir_path = os.getcwd()
#
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
else:
fmt = 'png'
if '-f' in sys.argv:
ind = sys.argv.index("-f")
filelist = [sys.argv[ind + 1]]
else:
filelist = os.listdir(dir_path)
## initialize some variables
samp_file = 'samples.txt'
azimuth_key = 'azimuth'
meas_file = 'measurements.txt'
loc_key = 'location'
loc_file = 'locations.txt'
method_key = 'method_codes'
dec_key = 'dir_dec'
inc_key = 'dir_inc'
tilt_corr_key = "dir_tilt_correction"
aniso_tilt_corr_key = "aniso_tilt_correction"
hyst_bcr_key = "hyst_bcr"
hyst_mr_key = "hyst_mr_moment"
hyst_ms_key = "hyst_ms_moment"
hyst_bc_key = "hyst_bc"
Mkeys = ['magnitude', 'magn_moment', 'magn_volume', 'magn_mass']
results_file = 'sites.txt'
hyst_file = 'specimens.txt'
aniso_file = 'specimens.txt'
# create contribution and propagate data throughout
con = cb.Contribution()
con.propagate_location_to_measurements()
con.propagate_location_to_specimens()
con.propagate_location_to_samples()
if not con.tables:
print('-E- No MagIC tables could be found in this directory')
error_log("No MagIC tables found")
return
# check to see if propagation worked, otherwise you can't plot by location
lowest_table = None
for table in con.ancestry:
if table in con.tables:
lowest_table = table
break
do_full_directory = False
# check that locations propagated down to the lowest table in the contribution
if 'location' in con.tables[lowest_table].df.columns:
# are there any locations in the lowest table?
if not all(con.tables[lowest_table].df['location'].isnull()):
locs = con.tables['locations'].df.index.unique()
lowest_locs = con.tables[lowest_table].df['location'].unique()
incorrect_locs = set(lowest_locs).difference(set(locs))
# are they actual locations?
if not incorrect_locs:
info_log(
'location names propagated to {}'.format(lowest_table))
else:
do_full_directory = True
error_log('location names did not propagate fully to {} table'.
format(lowest_table))
else:
do_full_directory = True
error_log(
'could not propagate location names down to {} table'.format(
lowest_table))
else:
do_full_directory = True
error_log('could not propagate location names down to {} table'.format(
lowest_table))
all_data = {}
all_data['measurements'] = con.tables.get('measurements', None)
all_data['specimens'] = con.tables.get('specimens', None)
all_data['samples'] = con.tables.get('samples', None)
all_data['sites'] = con.tables.get('sites', None)
all_data['locations'] = con.tables.get('locations', None)
locations = con.tables['locations'].df.index.unique()
dirlist = [loc for loc in locations if cb.not_null(loc) and loc != 'nan']
if not dirlist:
dirlist = ["./"]
if do_full_directory:
dirlist = ["./"]
# plot the whole contribution as one location
if dirlist == ["./"]:
error_log('plotting the entire contribution as one location')
for fname in os.listdir("."):
if fname.endswith(".txt"):
shutil.copy(fname, "tmp_" + fname)
# if possible, go through all data by location
# use tmp_*.txt files to separate out by location
for loc in dirlist:
print('\nworking on: ', loc)
def get_data(dtype, loc_name):
"""
Extract data of type dtype for location loc_name.
Write tmp_dtype.txt files if possible.
"""
if cb.not_null(all_data[dtype]):
data_container = all_data[dtype]
data_df = data_container.df[data_container.df['location'] ==
loc_name]
data = data_container.convert_to_pmag_data_list(df=data_df)
res = data_container.write_magic_file(
'tmp_{}.txt'.format(dtype), df=data_df)
if not res:
return []
return data
meas_data = get_data('measurements', loc)
spec_data = get_data('specimens', loc)
samp_data = get_data('samples', loc)
site_data = get_data('sites', loc)
location_data = get_data('locations', loc)
if loc == "./": # if you can't sort by location, do everything together
try:
meas_data = con.tables[
'measurements'].convert_to_pmag_data_list()
except KeyError:
meas_data = None
try:
spec_data = con.tables['specimens'].convert_to_pmag_data_list()
except KeyError:
spec_data = None
try:
samp_data = con.tables['samples'].convert_to_pmag_data_list()
except KeyError:
samp_data = None
try:
site_data = con.tables['sites'].convert_to_pmag_data_list()
except KeyError:
site_data = None
crd = 's'
if samp_file in filelist: # find coordinate systems
samps = samp_data
file_type = "samples"
# get all non blank sample orientations
Srecs = pmag.get_dictitem(samps, azimuth_key, '', 'F')
if len(Srecs) > 0:
crd = 'g'
print('using geographic coordinates')
else:
print('using specimen coordinates')
else:
if VERBOSE:
print('-I- No sample data found')
if meas_file in filelist: # start with measurement data
print('working on measurements data')
data = meas_data
file_type = 'measurements'
# looking for zeq_magic possibilities
# get all non blank method codes
AFZrecs = pmag.get_dictitem(data, method_key, 'LT-AF-Z', 'has')
# get all non blank method codes
TZrecs = pmag.get_dictitem(data, method_key, 'LT-T-Z', 'has')
# get all non blank method codes
MZrecs = pmag.get_dictitem(data, method_key, 'LT-M-Z', 'has')
# get all dec measurements
Drecs = pmag.get_dictitem(data, dec_key, '', 'F')
# get all inc measurements
Irecs = pmag.get_dictitem(data, inc_key, '', 'F')
for key in Mkeys:
Mrecs = pmag.get_dictitem(data, key, '',
'F') # get intensity data
if len(Mrecs) > 0:
break
# potential for stepwise demag curves
if len(AFZrecs) > 0 or len(TZrecs) > 0 or len(MZrecs) > 0 and len(
Drecs) > 0 and len(Irecs) > 0 and len(Mrecs) > 0:
CMD = 'zeq_magic.py -f tmp_measurements.txt -fsp tmp_specimens.txt -fsa tmp_samples.txt -fsi tmp_sites.txt -sav -fmt ' + fmt + ' -crd ' + crd
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-PI-TRM',
'has')) > 0:
CMD = 'thellier_magic.py -f tmp_measurements.txt -fsp tmp_specimens.txt -sav -fmt ' + fmt
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-HYS',
'has')) > 0: # find hyst experiments
# check for reqd columns
missing = check_for_reqd_cols(data, ['treat_temp'])
if missing:
error_log(
'LP-HYS method code present, but required column(s) [{}] missing'
.format(", ".join(missing)), loc, "quick_hyst.py")
else:
CMD = 'quick_hyst.py -f tmp_measurements.txt -sav -fmt ' + fmt
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# equal area plots of directional data
# at measurment level (by specimen)
if data:
missing = check_for_reqd_cols(data, ['dir_dec', 'dir_inc'])
if not missing:
CMD = "eqarea_magic.py -f tmp_measurements.txt -obj spc -sav -no-tilt -fmt " + fmt
print(CMD)
os.system(CMD)
info_log(CMD, loc, "eqarea_magic.py")
else:
if VERBOSE:
print('-I- No measurement data found')
# site data
if results_file in filelist:
print('-I- result file found', results_file)
data = site_data
file_type = 'sites'
print('-I- working on site directions')
print('number of datapoints: ', len(data), loc)
dec_key = 'dir_dec'
inc_key = 'dir_inc'
int_key = 'int_abs'
SiteDIs = pmag.get_dictitem(data, dec_key, "", 'F') # find decs
SiteDIs = pmag.get_dictitem(SiteDIs, inc_key, "",
'F') # find decs and incs
dir_data_found = len(SiteDIs)
print('{} Dec/inc pairs found'.format(dir_data_found))
# only individual results - not poles
# get only individual results (if result_type col is available)
if SiteDIs:
if 'result_type' in SiteDIs[0]:
SiteDIs = pmag.get_dictitem(SiteDIs, 'result_type', 'i',
'has')
# then convert tilt_corr_key to correct format
old_SiteDIs = SiteDIs
SiteDIs = []
for rec in old_SiteDIs:
if tilt_corr_key not in rec:
error_log(
"Directional data found, but missing {}, can't plot directions"
.format(tilt_corr_key), loc, "eqarea_magic.py")
break
if cb.is_null(
rec[tilt_corr_key]) and rec[tilt_corr_key] != 0:
rec[tilt_corr_key] = ""
else:
try:
rec[tilt_corr_key] = str(
int(float(rec[tilt_corr_key])))
except ValueError:
rec[tilt_corr_key] = ""
SiteDIs.append(rec)
print('number of individual directions: ', len(SiteDIs))
# tilt corrected coordinates
SiteDIs_t = pmag.get_dictitem(SiteDIs,
tilt_corr_key,
'100',
'T',
float_to_int=True)
print('number of tilt corrected directions: ', len(SiteDIs_t))
SiteDIs_g = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '0', 'T',
float_to_int=True) # geographic coordinates
print('number of geographic directions: ', len(SiteDIs_g))
SiteDIs_s = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '-1', 'T',
float_to_int=True) # sample coordinates
print('number of sample directions: ', len(SiteDIs_s))
SiteDIs_x = pmag.get_dictitem(SiteDIs, tilt_corr_key, '',
'T') # no coordinates
print('number of no coordinates directions: ', len(SiteDIs_x))
if len(SiteDIs_t) > 0 or len(SiteDIs_g) > 0 or len(
SiteDIs_s) > 0 or len(SiteDIs_x) > 0:
CRD = ""
if len(SiteDIs_t) > 0:
CRD = ' -crd t'
elif len(SiteDIs_g) > 0:
CRD = ' -crd g'
elif len(SiteDIs_s) > 0:
CRD = ' -crd s'
CMD = 'eqarea_magic.py -f tmp_sites.txt -fsp tmp_specimens.txt -fsa tmp_samples.txt -flo tmp_locations.txt -sav -fmt ' + fmt + CRD
print(CMD)
info_log(CMD, loc)
os.system(CMD)
else:
if dir_data_found:
error_log(
'{} dec/inc pairs found, but no equal area plots were made'
.format(dir_data_found), loc, "equarea_magic.py")
#
print('-I- working on VGP map')
VGPs = pmag.get_dictitem(SiteDIs, 'vgp_lat', "",
'F') # are there any VGPs?
if len(VGPs) > 0: # YES!
CMD = 'vgpmap_magic.py -f tmp_sites.txt -prj moll -res c -sym ro 5 -sav -fmt png'
print(CMD)
info_log(CMD, loc, 'vgpmap_magic.py')
os.system(CMD)
else:
print('-I- No vgps found')
print('-I- Look for intensities')
# is there any intensity data?
if site_data:
if int_key in site_data[0].keys():
# old way, wasn't working right:
#CMD = 'magic_select.py -key ' + int_key + ' 0. has -F tmp1.txt -f tmp_sites.txt'
Selection = pmag.get_dictkey(site_data, int_key, dtype="f")
with open('intensities.txt', 'w') as out:
for rec in Selection:
if rec != 0:
out.write(str(rec * 1e6) + "\n")
histfile = 'LO:_' + loc + \
'_TY:_intensities_histogram:_.' + fmt
# maybe run histplot.main here instead, so you can return an error message
CMD = "histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f intensities.txt -F " + histfile
os.system(CMD)
info_log(CMD, loc)
print(CMD)
else:
print('-I- No intensities found')
else:
print('-I- No intensities found')
##
if hyst_file in filelist:
print('working on hysteresis', hyst_file)
data = spec_data
file_type = 'specimens'
hdata = pmag.get_dictitem(data, hyst_bcr_key, '', 'F')
hdata = pmag.get_dictitem(hdata, hyst_mr_key, '', 'F')
hdata = pmag.get_dictitem(hdata, hyst_ms_key, '', 'F')
# there are data for a dayplot
hdata = pmag.get_dictitem(hdata, hyst_bc_key, '', 'F')
if len(hdata) > 0:
CMD = 'dayplot_magic.py -f tmp_specimens.txt -sav -fmt ' + fmt
info_log(CMD, loc)
print(CMD)
else:
print('no hysteresis data found')
if aniso_file in filelist: # do anisotropy plots if possible
print('working on anisotropy', aniso_file)
data = spec_data
file_type = 'specimens'
# make sure there is some anisotropy data
if not data:
print('No anisotropy data found')
elif 'aniso_s' not in data[0]:
print('No anisotropy data found')
else:
# get specimen coordinates
if aniso_tilt_corr_key not in data[0]:
sdata = data
else:
sdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'-1',
'T',
float_to_int=True)
# get specimen coordinates
gdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'0',
'T',
float_to_int=True)
# get specimen coordinates
tdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'100',
'T',
float_to_int=True)
CRD = ""
CMD = 'aniso_magic.py -x -B -sav -fmt ' + fmt
if len(sdata) > 3:
CMD = CMD + ' -crd s'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
if len(gdata) > 3:
CMD = CMD + ' -crd g'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
if len(tdata) > 3:
CMD = CMD + ' -crd t'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# remove temporary files
for fname in glob.glob('tmp*.txt'):
os.remove(fname)
try:
os.remove('intensities.txt')
except FileNotFoundError:
pass
if loc_file in filelist:
data, file_type = pmag.magic_read(loc_file) # read in location data
print('-I- working on pole map')
poles = pmag.get_dictitem(data, 'pole_lat', "",
'F') # are there any poles?
poles = pmag.get_dictitem(poles, 'pole_lon', "",
'F') # are there any poles?
if len(poles) > 0: # YES!
CMD = 'polemap_magic.py -sav -fmt png'
print(CMD)
info_log(CMD, "all locations", "polemap_magic.py")
os.system(CMD)
else:
print('-I- No poles found')
def main():
"""
NAME
mk_redo.py
DESCRIPTION
Makes thellier_redo and zeq_redo files from existing pmag_specimens format file
SYNTAX
mk_redo.py [-h] [command line options]
INPUT
takes specimens.txt formatted input file
OPTIONS
-h: prints help message and quits
-f FILE: specify input file, default is 'specimens.txt'
-F REDO: specify output file suffix, default is redo so that
output filenames are 'thellier_redo' for thellier data and 'zeq_redo' for direction only data
OUTPUT
makes a thellier_redo or a zeq_redo format file
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
zfile, tfile = 'zeq_redo', 'thellier_redo'
zredo, tredo = "", ""
dir_path = pmag.get_named_arg('-WD', '.')
inspec = pmag.get_named_arg('-f', 'specimens.txt')
if '-F' in sys.argv:
ind = sys.argv.index('-F')
redo = sys.argv[ind + 1]
tfile = redo
zfile = redo
inspec = pmag.resolve_file_name(inspec, dir_path)
zfile = pmag.resolve_file_name(zfile, dir_path)
tfile = pmag.resolve_file_name(tfile, dir_path)
#
# read in data
#
specs = []
prior_spec_data, file_type = pmag.magic_read(inspec)
if file_type != 'specimens':
print(file_type, " this is not a valid pmag_specimens file")
sys.exit()
outstrings = []
for spec in prior_spec_data:
tmp = spec["method_codes"].split(":")
meths = []
for meth in tmp:
methods = meth.strip().split('-')
for m in methods:
if m not in meths:
meths.append(m)
if 'DIR' in meths: # DE-BFL, DE-BFP or DE-FM
specs.append(spec['specimen'])
if 'dir_comp' in list(spec.keys()) and spec['dir_comp'] != "" and spec['dir_comp'] != " ":
comp_name = spec['dir_comp']
else:
comp_name = string.ascii_uppercase[specs.count(
spec['specimen']) - 1]
calculation_type = "DE-BFL" # assume default calculation type is best-fit line
if "BFP" in meths:
calculation_type = 'DE-BFP'
elif "FM" in meths:
calculation_type = 'DE-FM'
if zredo == "":
zredo = open(zfile, "w")
outstring = '%s %s %s %s %s \n' % (
spec["specimen"], calculation_type, spec["meas_step_min"], spec["meas_step_max"], comp_name)
if outstring not in outstrings:
zredo.write(outstring)
outstrings.append(outstring) # only writes unique interpretions
elif "PI" in meths and "TRM" in meths: # thellier record
if tredo == "":
tredo = open(tfile, "w")
outstring = '%s %i %i \n' % (spec["specimen"], float(
spec["meas_step_min"]), float(spec["meas_step_max"]))
if outstring not in outstrings:
tredo.write(outstring)
outstrings.append(outstring) # only writes unique interpretions
print('Redo files saved to: ', zfile, tfile)
def main():
"""
NAME
mst_magic.py
DESCRIPTION
converts MsT data (T,M) to magic_measurements format files
SYNTAX
mst_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify T,M format input file, required
-fsa SFILE: name with sample, site, location information
-F FILE: specify output file, default is MsT_measurements.txt
-dc H: specify applied field during measurement, default is 0.5 T
-syn : This is a synthetic specimen and has no sample/site/location information
-spn SPEC: specimen name
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT files:
T M: T is in Centigrade and M is uncalibrated magnitude
"""
# initialize some stuff
samp_con,Z="1","0"
dir_path='.'
citation='This study'
args=sys.argv
specnum,measnum=0,1
#
# get command line arguments
#
user=""
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
meas_file=dir_path+"/MsT_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
labfield='0.5'
if "-dc" in args:
ind=args.index("-dc")
labfield=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(samp_file)
if '-f' in args:
ind=args.index("-f")
infile=dir_path+'/'+args[ind+1]
try:
input=open(infile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print main.__doc__
print "-f is required option"
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
er_location_name,syn,specimen_name='unknown',0,'unknown'
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-spn" in args:
ind=args.index("-spn")
specimen_name=args[ind+1]
else:
print main.__doc__
print "-spn is required option"
sys.exit()
if "-syn" in args: syn=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
samp_con=sys.argv[ind+1]
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
MagRecs,specs=[],[]
version_num=pmag.get_version()
data=input.readlines()
T0=float(data[0].split()[0])
for line in data:
instcode=""
if len(line)>1:
MagRec={}
if syn==0: MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_dc_field"]=labfield
rec=line.split()
T=float(rec[0])
MagRec["measurment_temp"]='%8.3e' % (float(rec[0])+273.) # temp in kelvin
if T>T0:
MagRec["magic_method_codes"]='LP-MW-I'
elif T<T0:
MagRec["magic_method_codes"]='LP-MC-I'
T0=T
else:
print 'skipping repeated temperature step'
MagRec["magic_method_codes"]=''
T0=T
MagRec["measurement_magnitude"]='%10.3e'% (float(rec[1])) # uncalibrated magnitude
if syn==0:
MagRec["er_specimen_name"]=specimen_name
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=specimen_name[:specnum]
else:
MagRec["er_sample_name"]=specimen_name
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
else:
MagRec["er_synthetic_name"]=specimen_name
MagRec["er_location_name"]=""
MagRec["er_sample_name"]=""
MagRec["er_site_name"]=""
MagRec["er_specimen_name"]=""
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["measurement_flag"]='g'
MagRec["measurement_number"]=str(measnum)
measnum+=1
MagRecs.append(MagRec)
for rec in MagRecs: # sort out the measurements by experiment type
rec['magic_experiment_name']=specimen_name
if rec['magic_method_codes']=='LP-MW-I':
rec["magic_experiment_name"]=specimen_name+':LP-MW-I:Curie'
elif rec['magic_method_codes']=='LP-MC-I':
rec["magic_experiment_name"]=specimen_name+':LP-MC-I'
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "results put in ",meas_file
def convert(**kwargs):
# initialize some stuff
methcode="LP-NO"
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD=0,0
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
missing=1
demag="N"
citations='This study'
fmt='old'
Samps=[]
trm=0
irm=0
#get args
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file', '')
labfield = kwargs.get('labfield', '')
if labfield:
labfield = float(labfield) *1e-6
else:
labfield = 0
phi = kwargs.get('phi', 0)
if phi:
phi = float(phi)
else:
phi = 0
theta = kwargs.get('theta', 0)
if theta:
theta=float(theta)
else:
theta = 0
peakfield = kwargs.get('peakfield', 0)
if peakfield:
peakfield=float(peakfield) *1e-3
else:
peakfield = 0
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
samp_infile = kwargs.get('samp_infile', '')
syn = kwargs.get('syn', 0)
institution = kwargs.get('institution', '')
syntype = kwargs.get('syntype', '')
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 0)
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
cooling_rates = kwargs.get('cooling_rates', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
timezone = kwargs.get('timezone', 'UTC')
# make sure all initial values are correctly set up (whether they come from the command line or a GUI)
if samp_infile:
Samps, file_type = pmag.magic_read(samp_infile)
if coil:
coil = str(coil)
methcode="LP-IRM"
irmunits = "V"
if coil not in ["1","2","3"]:
print(__doc__)
print('not a valid coil specification')
return False, '{} is not a valid coil specification'.format(coil)
if mag_file:
lines = pmag.open_file(mag_file)
if not lines:
print("you must provide a valid mag_file")
return False, "you must provide a valid mag_file"
if not mag_file:
print(__doc__)
print("mag_file field is required option")
return False, "mag_file field is required option"
if specnum!=0:
specnum=-specnum
if "4" == samp_con[0]:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
print('---------------')
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" == samp_con[0]:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z = 0
if codelist:
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in sys.argv: methcode="LT-AF-Z"
if'-dc' in sys.argv: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in sys.argv: methcode="LT-T-Z"
if '-dc' in sys.argv: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "I3d" in codes:
methcode="LT-T-Z:LP-IRM-3D"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if "CR" in codes:
demag="T"
cooling_rate_experiment=1
if command_line:
ind=sys.argv.index("CR")
cooling_rates=sys.argv[ind+1]
cooling_rates_list=cooling_rates.split(',')
else:
cooling_rates_list=str(cooling_rates).split(',')
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="T" and "CR" in codes:
methcode="LP-CR-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
version_num=pmag.get_version()
##################################
for line in lines:
instcode=""
if len(line)>2:
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
MeasRec['software_packages']=version_num
MeasRec["description"]=""
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
try: float(rec[0]); print("No specimen name for line #%d in the measurement file"%lines.index(line)); continue
except ValueError: pass
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if methcode=="LP-IRM":
if irmunits=='mT':
labfield=float(treat[0])*1e-3
else:
labfield=pmag.getfield(irmunits,coil,treat[0])
if rec[1][0]!="-":
phi,theta=0.,90.
else:
phi,theta=0.,-90.
meas_type="LT-IRM"
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
if len(rec)>6:
code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time
if len(code1)==2: # old format with AM/PM
missing=0
code2=code1[0].split('/') # break date into mon/day/year
code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements
yy=int(code2[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(code2[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(code2[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if code3[0]=="PM":hh=hh+12
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
dt=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00"
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
MeasRec["timestamp"]=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
if inst=="":
if code3[1][0]=='C':instcode='SIO-bubba'
if code3[1][0]=='G':instcode='SIO-flo'
else:
instcode=''
MeasRec["meas_n_orient"]=code3[1][2]
elif len(code1)>2: # newest format (cryo7 or later)
if "LP-AN-ARM" not in methcode:labfield=0
fmt='new'
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else:
min=str(min)
dt=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00"
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
MeasRec["timestamp"]=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
if inst=="":
if code1[6][0]=='C':
instcode='SIO-bubba'
if code1[6][0]=='G':
instcode='SIO-flo'
else:
instcode=''
if len(code1)>1:
MeasRec["meas_n_orient"]=code1[6][2]
else:
MeasRec["meas_n_orient"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C':
demag="T"
if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6
if code1[2]=='mT' and methcode!="LP-IRM":
demag="AF"
if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6
if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM":
phi,theta=0.,-90.
if demag=="T": meas_type="LT-T-I"
if demag=="AF": meas_type="LT-AF-I"
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
if code1[4]=='' or labfield==0. and meas_type!="LT-IRM":
if demag=='T':meas_type="LT-T-Z"
if demag=="AF":meas_type="LT-AF-Z"
MeasRec["treat_dc_field"]='0'
if syn==0:
specimen=rec[0]
MeasRec["specimen"]=specimen
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
if samp_infile and Samps: # if samp_infile was provided AND yielded sample data
samp=pmag.get_dictitem(Samps,'sample',sample,'T')
if len(samp)>0:
location=samp[0]["location"]
site=samp[0]["site"]
else:
location=''
site=''
else:
site=pmag.parse_site(sample,samp_con,Z)
if location!='' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
if site!='' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]:
SiteRec['location'] = location
SiteRec['site'] = site
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if sample!='' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]:
SampRec['site'] = site
SampRec['sample'] = sample
SampRecs.append(SampRec)
if specimen!='' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]:
SpecRec["specimen"]=specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
else:
specimen=rec[0]
MeasRec["specimen"]=specimen
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
site=pmag.parse_site(sample,samp_con,Z)
if location!='' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
if site!='' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]:
SiteRec['location'] = location
SiteRec['site'] = site
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if sample!='' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]:
SampRec['site'] = site
SampRec['sample'] = sample
SampRecs.append(SampRec)
if specimen!='' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]:
SpecRec["specimen"]=specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
SampRec["institution"]=institution
SampRec["material_type"]=syntype
if float(rec[1])==0:
pass
elif demag=="AF":
if methcode != "LP-AN-ARM":
MeasRec["treat_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
if meas_type=="LT-AF-Z": MeasRec["treat_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z:LP-AN-ARM:"
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(0)
if labfield!=0 and methcode!="LP-AN-ARM": print("Warning - inconsistency in mag file with lab field - overriding file with 0")
else:
meas_type="LT-AF-I:LP-AN-ARM"
ipos=int(treat[0])-1
MeasRec["treat_dc_field_phi"]='%7.1f' %(dec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (inc[ipos])
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T" and methcode == "LP-AN-TRM":
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-AN-TRM"
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
else:
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-AN-TRM"
else:
meas_type="LT-T-I:LP-AN-TRM"
# find the direction of the lab field in two ways:
# (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z)
ipos_code=int(treat[1][0])-1
# (2) using the magnetization
DEC=float(rec[4])
INC=float(rec[5])
if INC < 45 and INC > -45:
if DEC>315 or DEC<45: ipos_guess=0
if DEC>45 and DEC<135: ipos_guess=1
if DEC>135 and DEC<225: ipos_guess=3
if DEC>225 and DEC<315: ipos_guess=4
else:
if INC >45: ipos_guess=2
if INC <-45: ipos_guess=5
# prefer the guess over the code
ipos=ipos_guess
MeasRec["treat_dc_field_phi"]='%7.1f' %(tdec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (tinc[ipos])
# check it
if ipos_guess!=ipos_code and treat[1][0]!='7':
print("-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat))))
elif demag=="S": # Shaw experiment
if treat[1][1]=='0':
if int(treat[0])!=0:
MeasRec["treat_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z" # first AF
else:
meas_type="LT-NO"
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
elif treat[1][1]=='1':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(arm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='2':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='%8.3e'%(trm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
MeasRec["treat_temp"]='%8.3e' % (trm_peakT)
meas_type="LT-T-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='3':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(arm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
# Cooling rate experient # added by rshaar
elif demag=="T" and methcode == "LP-CR-TRM":
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-CR-TRM"
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
else:
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-CR-TRM"
else:
meas_type="LT-T-I:LP-CR-TRM"
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
indx=int(treat[1][0])-1
# alteration check matjed as 0.7 in the measurement file
if indx==6:
cooling_time= cooling_rates_list[-1]
else:
cooling_time=cooling_rates_list[indx]
MeasRec["description"]="cooling_rate"+":"+cooling_time+":"+"K/min"
elif demag!='N':
if len(treat)==1:treat.append('0')
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MeasRec["treat_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
labfield=float(treat[1])*1e-6
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
meas_type="LT-T-I:LP-TRM" # trm acquisition experiment
MeasRec["dir_csd"]=rec[2]
MeasRec["magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MeasRec["dir_dec"]=rec[4]
MeasRec["dir_inc"]=rec[5]
MeasRec["instrument_codes"]=instcode
MeasRec["analysts"]=user
MeasRec["citations"]=citations
if "LP-IRM-3D" in methcode : meas_type=methcode
#MeasRec["method_codes"]=methcode.strip(':')
MeasRec["method_codes"]=meas_type
MeasRec["quality"]='g'
if 'std' in rec[0]:
MeasRec["standard"]='s'
else:
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
#print MeasRec['treat_temp']
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
# create MagIC tables
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
# write MagIC tables to file
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a pmag_results table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE pmag_results format file, [default is pmag_results.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: pmag_results.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
dir_path = '.'
res, ages = 'c', 0
plot = 0
proj = 'ortho'
results_file = 'pmag_results.txt'
ell, flip = 0, 0
lat_0, lon_0 = 90., 0.
fmt = 'pdf'
sym, size = 'ro', 8
rsym, rsize = 'g^', 8
anti = 0
fancy = 0
coord = ""
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-S' in sys.argv:
anti = 1
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind+1]
if '-sav' in sys.argv:
plot = 1
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res = sys.argv[ind+1]
if '-etp' in sys.argv:
fancy = 1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj = sys.argv[ind+1]
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind+1])
rsize = int(sys.argv[ind+2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind+1])
size = int(sys.argv[ind+2])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind+1])
lon_0 = float(sys.argv[ind+2])
if '-ell' in sys.argv:
ell = 1
if '-age' in sys.argv:
ages = 1
if '-f' in sys.argv:
ind = sys.argv.index('-f')
results_file = sys.argv[ind+1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind+1]
if crd == 'g':
coord = '0'
if crd == 't':
coord = '100'
results_file = dir_path+'/'+results_file
data, file_type = pmag.magic_read(results_file)
if file_type != 'pmag_results':
print("bad results file")
sys.exit()
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
lats, lons, dp, dm, a95 = [], [], [], [], []
Pars = []
dates, rlats, rlons = [], [], []
if 'data_type' in data[0].keys():
# get all site level data
Results = pmag.get_dictitem(data, 'data_type', 'i', 'T')
else:
Results = data
# get all non-blank latitudes
Results = pmag.get_dictitem(Results, 'vgp_lat', '', 'F')
# get all non-blank longitudes
Results = pmag.get_dictitem(Results, 'vgp_lon', '', 'F')
if coord != "":
# get specified coordinate system
Results = pmag.get_dictitem(Results, 'tilt_correction', coord, 'T')
location = ""
for rec in Results:
if rec['er_location_names'] not in location:
location = location+':'+rec['er_location_names']
if 'average_age' in rec.keys() and rec['average_age'] != "" and ages == 1:
dates.append(rec['average_age'])
lat = float(rec['vgp_lat'])
lon = float(rec['vgp_lon'])
if flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon+180.
if lon > 360:
lon = lon-360.
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
elif anti == 1:
lats.append(-lat)
lon = lon+180.
if lon > 360:
lon = lon-360.
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'vgp_dm' in rec.keys() and rec['vgp_dm'] != "":
ell1 = float(rec['vgp_dm'])
if 'vgp_dp' in rec.keys() and rec['vgp_dp'] != "":
ell2 = float(rec['vgp_dp'])
if 'vgp_alpha95' in rec.keys() and rec['vgp_alpha95'] != "":
ell1, ell2 = float(rec['vgp_alpha95']), float(rec['vgp_alpha95'])
if ell1 != "" and ell2 != "":
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = abs(lats[-1])/lats[-1]
ppars.append(lats[-1]-isign*90.)
ppars.append(ell2)
ppars.append(lons[-1]+90.)
ppars.append(0.)
Pars.append(ppars)
location = location.strip(':')
Opts = {'latmin': -90, 'latmax': 90, 'lonmin': 0., 'lonmax': 360., 'lat_0': lat_0, 'lon_0': lon_0,
'proj': proj, 'sym': 'bs', 'symsize': 3, 'pltgrid': 0, 'res': res, 'boundinglat': 0.}
Opts['details'] = {'coasts': 1, 'rivers': 0, 'states': 0,
'countries': 0, 'ocean': 1, 'fancy': fancy}
# make the base map with a blue triangle at the pole`
pmagplotlib.plot_map(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
Opts['names'] = []
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], rlats, rlons, Opts)
if plot == 0:
pmagplotlib.draw_figs(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {'coasts': 0, 'rivers': 0,
'states': 0, 'countries': 0, 'ocean': 0}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plot_ell(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole`
pmagplotlib.plot_map(FIG['map'], elats, elons, Opts)
if plot == 0:
pmagplotlib.draw_figs(FIG)
files = {}
for key in FIG.keys():
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_'+location+'_VGP_map.'+fmt
else: # use more readable plot naming convention
files[key] = '{}_VGP_map.{}'.format(
location.replace(' ', '_'), fmt)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'LO:_'+location+'_VGP_map'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
print("Good bye")
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
foldtest_magic.py
DESCRIPTION
does a fold test (Tauxe, 2010) on data
INPUT FORMAT
pmag_specimens format file, er_samples.txt format file (for bedding)
SYNTAX
foldtest_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f sites formatted file [default for 3.0 is sites.txt, for 2.5, pmag_sites.txt]
-fsa samples formatted file
-fsi sites formatted file
-exc use criteria to set acceptance criteria (supported only for data model 3)
-n NB, set number of bootstraps, default is 1000
-b MIN, MAX, set bounds for untilting, default is -10, 150
-fmt FMT, specify format - default is svg
-sav saves plots and quits
-DM NUM MagIC data model number (2 or 3, default 3)
OUTPUT
Geographic: is an equal area projection of the input data in
original coordinates
Stratigraphic: is an equal area projection of the input data in
tilt adjusted coordinates
% Untilting: The dashed (red) curves are representative plots of
maximum eigenvalue (tau_1) as a function of untilting
The solid line is the cumulative distribution of the
% Untilting required to maximize tau for all the
bootstrapped data sets. The dashed vertical lines
are 95% confidence bounds on the % untilting that yields
the most clustered result (maximum tau_1).
Command line: prints out the bootstrapped iterations and
finally the confidence bounds on optimum untilting.
If the 95% conf bounds include 0, then a pre-tilt magnetization is indicated
If the 95% conf bounds include 100, then a post-tilt magnetization is indicated
If the 95% conf bounds exclude both 0 and 100, syn-tilt magnetization is
possible as is vertical axis rotation or other pathologies
"""
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
kappa = 0
dir_path = pmag.get_named_arg("-WD", ".")
nboot = int(float(pmag.get_named_arg("-n", 1000))) # number of bootstraps
fmt = pmag.get_named_arg("-fmt", "svg")
data_model_num = int(float(pmag.get_named_arg("-DM", 3)))
if data_model_num == 3:
infile = pmag.get_named_arg("-f", 'sites.txt')
orfile = 'samples.txt'
site_col = 'site'
dec_col = 'dir_dec'
inc_col = 'dir_inc'
tilt_col = 'dir_tilt_correction'
dipkey, azkey = 'bed_dip', 'bed_dip_direction'
crit_col = 'criterion'
critfile = 'criteria.txt'
else:
infile = pmag.get_named_arg("-f", 'pmag_sites.txt')
orfile = 'er_samples.txt'
site_col = 'er_site_name'
dec_col = 'site_dec'
inc_col = 'site_inc'
tilt_col = 'site_tilt_correction'
dipkey, azkey = 'sample_bed_dip', 'sample_bed_dip_direction'
crit_col = 'pmag_criteria_code'
critfile = 'pmag_criteria.txt'
if '-sav' in sys.argv:
plot = 1
else:
plot = 0
if '-b' in sys.argv:
ind = sys.argv.index('-b')
untilt_min = int(sys.argv[ind+1])
untilt_max = int(sys.argv[ind+2])
else:
untilt_min, untilt_max = -10, 150
if '-fsa' in sys.argv:
orfile = pmag.get_named_arg("-fsa", "")
elif '-fsi' in sys.argv:
orfile = pmag.get_named_arg("-fsi", "")
if data_model_num == 3:
dipkey, azkey = 'bed_dip', 'bed_dip_direction'
else:
dipkey, azkey = 'site_bed_dip', 'site_bed_dip_direction'
else:
if data_model_num == 3:
orfile = 'sites.txt'
else:
orfile = 'pmag_sites.txt'
orfile = pmag.resolve_file_name(orfile, dir_path)
infile = pmag.resolve_file_name(infile, dir_path)
critfile = pmag.resolve_file_name(critfile, dir_path)
df = pd.read_csv(infile, sep='\t', header=1)
# keep only records with tilt_col
data = df.copy()
data = data[data[tilt_col].notnull()]
data = data.where(data.notnull(), "")
# turn into pmag data list
data = list(data.T.apply(dict))
# get orientation data
if data_model_num == 3:
# often orientation will be in infile (sites table)
if os.path.split(orfile)[1] == os.path.split(infile)[1]:
ordata = df[df[azkey].notnull()]
ordata = ordata[ordata[dipkey].notnull()]
ordata = list(ordata.T.apply(dict))
# sometimes orientation might be in a sample file instead
else:
ordata = pd.read_csv(orfile, sep='\t', header=1)
ordata = list(ordata.T.apply(dict))
else:
ordata, file_type = pmag.magic_read(orfile)
if '-exc' in sys.argv:
crits, file_type = pmag.magic_read(critfile)
SiteCrits = []
for crit in crits:
if crit[crit_col] == "DE-SITE":
SiteCrits.append(crit)
#break
# get to work
#
PLTS = {'geo': 1, 'strat': 2, 'taus': 3} # make plot dictionary
if not set_env.IS_WIN:
pmagplotlib.plot_init(PLTS['geo'], 5, 5)
pmagplotlib.plot_init(PLTS['strat'], 5, 5)
pmagplotlib.plot_init(PLTS['taus'], 5, 5)
if data_model_num == 2:
GEOrecs = pmag.get_dictitem(data, tilt_col, '0', 'T')
else:
GEOrecs = data
if len(GEOrecs) > 0: # have some geographic data
num_dropped = 0
DIDDs = [] # set up list for dec inc dip_direction, dip
for rec in GEOrecs: # parse data
dip, dip_dir = 0, -1
Dec = float(rec[dec_col])
Inc = float(rec[inc_col])
orecs = pmag.get_dictitem(
ordata, site_col, rec[site_col], 'T')
if len(orecs) > 0:
if orecs[0][azkey] != "":
dip_dir = float(orecs[0][azkey])
if orecs[0][dipkey] != "":
dip = float(orecs[0][dipkey])
if dip != 0 and dip_dir != -1:
if '-exc' in sys.argv:
keep = 1
for site_crit in SiteCrits:
crit_name = site_crit['table_column'].split('.')[1]
if crit_name and crit_name in rec.keys() and rec[crit_name]:
# get the correct operation (<, >=, =, etc.)
op = OPS[site_crit['criterion_operation']]
# then make sure the site record passes
if op(float(rec[crit_name]), float(site_crit['criterion_value'])):
keep = 0
if keep == 1:
DIDDs.append([Dec, Inc, dip_dir, dip])
else:
num_dropped += 1
else:
DIDDs.append([Dec, Inc, dip_dir, dip])
if num_dropped:
print("-W- Dropped {} records because each failed one or more criteria".format(num_dropped))
else:
print('no geographic directional data found')
sys.exit()
pmagplotlib.plot_eq(PLTS['geo'], DIDDs, 'Geographic')
data = np.array(DIDDs)
D, I = pmag.dotilt_V(data)
TCs = np.array([D, I]).transpose()
pmagplotlib.plot_eq(PLTS['strat'], TCs, 'Stratigraphic')
if plot == 0:
pmagplotlib.draw_figs(PLTS)
Percs = list(range(untilt_min, untilt_max))
Cdf, Untilt = [], []
plt.figure(num=PLTS['taus'])
print('doing ', nboot, ' iterations...please be patient.....')
for n in range(nboot): # do bootstrap data sets - plot first 25 as dashed red line
if n % 50 == 0:
print(n)
Taus = [] # set up lists for taus
PDs = pmag.pseudo(DIDDs)
if kappa != 0:
for k in range(len(PDs)):
d, i = pmag.fshdev(kappa)
dipdir, dip = pmag.dodirot(d, i, PDs[k][2], PDs[k][3])
PDs[k][2] = dipdir
PDs[k][3] = dip
for perc in Percs:
tilt = np.array([1., 1., 1., 0.01*perc])
D, I = pmag.dotilt_V(PDs*tilt)
TCs = np.array([D, I]).transpose()
ppars = pmag.doprinc(TCs) # get principal directions
Taus.append(ppars['tau1'])
if n < 25:
plt.plot(Percs, Taus, 'r--')
# tilt that gives maximum tau
Untilt.append(Percs[Taus.index(np.max(Taus))])
Cdf.append(float(n) / float(nboot))
plt.plot(Percs, Taus, 'k')
plt.xlabel('% Untilting')
plt.ylabel('tau_1 (red), CDF (green)')
Untilt.sort() # now for CDF of tilt of maximum tau
plt.plot(Untilt, Cdf, 'g')
lower = int(.025*nboot)
upper = int(.975*nboot)
plt.axvline(x=Untilt[lower], ymin=0, ymax=1, linewidth=1, linestyle='--')
plt.axvline(x=Untilt[upper], ymin=0, ymax=1, linewidth=1, linestyle='--')
tit = '%i - %i %s' % (Untilt[lower], Untilt[upper], 'Percent Unfolding')
print(tit)
plt.title(tit)
if plot == 0:
pmagplotlib.draw_figs(PLTS)
ans = input('S[a]ve all figures, <Return> to quit \n ')
if ans != 'a':
print("Good bye")
sys.exit()
files = {}
for key in list(PLTS.keys()):
files[key] = ('foldtest_'+'%s' % (key.strip()[:2])+'.'+fmt)
pmagplotlib.save_plots(PLTS, files)
def main():
"""
NAME
dayplot_magic.py
DESCRIPTION
makes 'day plots' (Day et al. 1977) and squareness/coercivity,
plots 'linear mixing' curve from Dunlop and Carter-Stiglitz (2006).
squareness coercivity of remanence (Neel, 1955) plots after
Tauxe et al. (2002)
SYNTAX
dayplot_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input hysteresis file, default is rmag_hysteresis.txt
-fr: specify input remanence file, default is rmag_remanence.txt
-fmt [svg,png,jpg] format for output plots
-sav saves plots and quits quietly
-n label specimen names
"""
args = sys.argv
hyst_file, rem_file = "rmag_hysteresis.txt", "rmag_remanence.txt"
dir_path = '.'
verbose = pmagplotlib.verbose
fmt = 'svg' # default file format
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-f' in args:
ind = args.index("-f")
hyst_file = args[ind + 1]
if '-fr' in args:
ind = args.index("-fr")
rem_file = args[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-sav' in sys.argv:
plots = 1
verbose = 0
else:
plots = 0
if '-n' in sys.argv:
label = 1
else:
label = 0
hyst_file = os.path.realpath(os.path.join(dir_path, hyst_file))
rem_file = os.path.realpath(os.path.join(dir_path, rem_file))
#
# initialize some variables
# define figure numbers for Day,S-Bc,S-Bcr
DSC = {}
DSC['day'], DSC['S-Bc'], DSC['S-Bcr'], DSC['bcr1-bcr2'] = 1, 2, 3, 4
pmagplotlib.plot_init(DSC['day'], 5, 5)
pmagplotlib.plot_init(DSC['S-Bc'], 5, 5)
pmagplotlib.plot_init(DSC['S-Bcr'], 5, 5)
pmagplotlib.plot_init(DSC['bcr1-bcr2'], 5, 5)
#
#
hyst_data, file_type = pmag.magic_read(hyst_file)
rem_data, file_type = pmag.magic_read(rem_file)
#
S, BcrBc, Bcr2, Bc, hsids, Bcr = [], [], [], [], [], []
Ms, Bcr1, Bcr1Bc, S1 = [], [], [], []
names = []
locations = ''
for rec in hyst_data:
if 'er_location_name' in rec.keys(
) and rec['er_location_name'] not in locations:
locations = locations + rec['er_location_name'] + '_'
if rec['hysteresis_bcr'] != "" and rec['hysteresis_mr_moment'] != "":
S.append(
float(rec['hysteresis_mr_moment']) /
float(rec['hysteresis_ms_moment']))
Bcr.append(float(rec['hysteresis_bcr']))
Bc.append(float(rec['hysteresis_bc']))
BcrBc.append(Bcr[-1] / Bc[-1])
if 'er_synthetic_name' in rec.keys(
) and rec['er_synthetic_name'] != "":
rec['er_specimen_name'] = rec['er_synthetic_name']
hsids.append(rec['er_specimen_name'])
names.append(rec['er_specimen_name'])
if len(rem_data) > 0:
for rec in rem_data:
if rec['remanence_bcr'] != "" and float(rec['remanence_bcr']) > 0:
try:
ind = hsids.index(rec['er_specimen_name'])
Bcr1.append(float(rec['remanence_bcr']))
Bcr1Bc.append(Bcr1[-1] / Bc[ind])
S1.append(S[ind])
Bcr2.append(Bcr[ind])
except ValueError:
if verbose:
print('hysteresis data for ', rec['er_specimen_name'],
' not found')
#
# now plot the day and S-Bc, S-Bcr plots
#
leglist = []
if label == 0: names = []
if len(Bcr1) > 0:
pmagplotlib.plotDay(DSC['day'], Bcr1Bc, S1, 'ro', names=names)
pmagplotlib.plotSBcr(DSC['S-Bcr'], Bcr1, S1, 'ro')
pmagplotlib.plot_init(DSC['bcr1-bcr2'], 5, 5)
pmagplotlib.plotBcr(DSC['bcr1-bcr2'], Bcr1, Bcr2)
else:
del DSC['bcr1-bcr2']
pmagplotlib.plotDay(DSC['day'], BcrBc, S, 'bs', names=names)
pmagplotlib.plotSBcr(DSC['S-Bcr'], Bcr, S, 'bs')
pmagplotlib.plotSBc(DSC['S-Bc'], Bc, S, 'bs')
files = {}
if len(locations) > 0: locations = locations[:-1]
for key in DSC.keys():
if pmagplotlib.isServer: # use server plot naming convention
files[
key] = 'LO:_' + locations + '_' + 'SI:__SA:__SP:__TY:_' + key + '_.' + fmt
else: # use more readable plot naming convention
files[key] = '{}_{}.{}'.format(locations, key, fmt)
if verbose:
pmagplotlib.drawFIGS(DSC)
ans = raw_input(" S[a]ve to save plots, return to quit: ")
if ans == "a":
pmagplotlib.saveP(DSC, files)
else:
sys.exit()
if plots: pmagplotlib.saveP(DSC, files)
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
-sav save plots and quit
-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,plt,plot='svg',1,0
Crits=""
M,N,acutoff,kcutoff=180.,1,180.,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 '-exc' in sys.argv:
Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt')
for crit in Crits:
if 'specimen_mad' in crit: M=float(crit['specimen_mad'])
if 'specimen_n' in crit: N=float(crit['specimen_n'])
if 'site_alpha95' in crit: acutoff=float(crit['site_alpha95'])
if 'site_k' in crit: kcutoff=float(crit['site_k'])
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:plt=0
if '-sav' in sys.argv:plot=1
#
in_file=dir_path+'/'+in_file
Specs,file_type=pmag.magic_read(in_file)
if file_type!='pmag_specimens':
print('Error opening file')
sys.exit()
sitelist=[]
for rec in Specs:
if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
sitelist.sort()
if plt==1:
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 list(spec.keys()):spec['specimen_tilt_correction']='-1' # assume unoriented
if spec['er_site_name']==site:
if 'specimen_mad' not in list(spec.keys()) or spec['specimen_mad']=="":
if 'specimen_alpha95' in list(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 list(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 plt==1:
files={}
files['eqarea']=site+'_'+crd+'_'+'eqarea'+'.'+fmt
pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
if plot==0:
pmagplotlib.drawFIGS(EQ)
ans=input("s[a]ve plot, [q]uit, <return> to continue:\n ")
if ans=="a":
pmagplotlib.saveP(EQ,files)
if ans=="q": sys.exit()
else:
pmagplotlib.saveP(EQ,files)
else:
print('skipping site - not enough data with specified coordinate system')
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path = "."
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
args = sys.argv
ipar, ihext, ivec, iboot, imeas, isite, iplot, vec = 0, 0, 0, 1, 1, 0, 1, 0
hpars, bpars, PDir = [], [], []
CS, crd = '-1', 's'
nb = 1000
fmt = 'pdf'
ResRecs = []
orlist = []
outfile, comp, Dir, gtcirc, PDir = 'rmag_results.txt', 0, [], 0, []
infile = 'rmag_anisotropy.txt'
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if '-nb' in args:
ind = args.index('-nb')
nb = int(args[ind + 1])
if '-usr' in args:
ind = args.index('-usr')
user = args[ind + 1]
else:
user = ""
if '-B' in args: iboot, ihext = 0, 1
if '-par' in args: ipar = 1
if '-x' in args: ihext = 1
if '-v' in args: ivec = 1
if '-sit' in args: isite = 1
if '-P' in args: iplot = 0
if '-f' in args:
ind = args.index('-f')
infile = args[ind + 1]
if '-F' in args:
ind = args.index('-F')
outfile = args[ind + 1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind + 1]
if crd == 'g': CS = '0'
if crd == 't': CS = '100'
if '-fmt' in args:
ind = args.index('-fmt')
fmt = args[ind + 1]
if '-sav' in args:
plots = 1
verbose = 0
else:
plots = 0
if '-gtc' in args:
ind = args.index('-gtc')
d, i = float(args[ind + 1]), float(args[ind + 2])
PDir.append(d)
PDir.append(i)
if '-d' in args:
comp = 1
ind = args.index('-d')
vec = int(args[ind + 1]) - 1
Dir = [float(args[ind + 2]), float(args[ind + 3])]
#
# set up plots
#
if infile[0] != '/': infile = dir_path + '/' + infile
if outfile[0] != '/': outfile = dir_path + '/' + outfile
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS['data'], ANIS['conf'] = 1, 2
if iboot == 1:
ANIS['tcdf'] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS['conf'], 5, 5)
pmagplotlib.plot_init(ANIS['data'], 5, 5)
# read in the data
data, ifiletype = pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if 'anisotropy_tilt_correction' not in rec.keys():
rec['anisotropy_tilt_correction'] = '-1'
if rec['anisotropy_tilt_correction'] not in orlist:
orlist.append(rec['anisotropy_tilt_correction'])
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = '-1'
if CS == '-1': crd = 's'
if CS == '0': crd = 'g'
if CS == '100': crd = 't'
if verbose:
print("desired coordinate system not available, using available: ",
crd)
if isite == 1:
sitelist = []
for rec in data:
if rec['er_site_name'] not in sitelist:
sitelist.append(rec['er_site_name'])
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
sdata, Ss = [], [] # list of S format data
Locs, Sites, Samples, Specimens, Cits = [], [], [], [], []
if isite == 0:
sdata = data
else:
site = sitelist[k]
for rec in data:
if rec['er_site_name'] == site: sdata.append(rec)
anitypes = []
csrecs = pmag.get_dictitem(sdata, 'anisotropy_tilt_correction', CS,
'T')
for rec in csrecs:
if rec['anisotropy_type'] not in anitypes:
anitypes.append(rec['anisotropy_type'])
if rec['er_location_name'] not in Locs:
Locs.append(rec['er_location_name'])
if rec['er_site_name'] not in Sites:
Sites.append(rec['er_site_name'])
if rec['er_sample_name'] not in Samples:
Samples.append(rec['er_sample_name'])
if rec['er_specimen_name'] not in Specimens:
Specimens.append(rec['er_specimen_name'])
if rec['er_citation_names'] not in Cits:
Cits.append(rec['er_citation_names'])
s = []
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0] <= 1.0: Ss.append(s) # protect against crap
#tau,Vdirs=pmag.doseigs(s)
ResRec = {}
ResRec['er_location_names'] = rec['er_location_name']
ResRec['er_citation_names'] = rec['er_citation_names']
ResRec['er_site_names'] = rec['er_site_name']
ResRec['er_sample_names'] = rec['er_sample_name']
ResRec['er_specimen_names'] = rec['er_specimen_name']
ResRec['rmag_result_name'] = rec['er_specimen_name'] + ":" + rec[
'anisotropy_type']
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
ResRec["anisotropy_type"] = rec['anisotropy_type']
if "anisotropy_n" not in rec.keys(): rec["anisotropy_n"] = "6"
if "anisotropy_sigma" not in rec.keys():
rec["anisotropy_sigma"] = "0"
fpars = pmag.dohext(
int(rec["anisotropy_n"]) - 6, float(rec["anisotropy_sigma"]),
s)
ResRec["anisotropy_v1_dec"] = '%7.1f' % (fpars['v1_dec'])
ResRec["anisotropy_v2_dec"] = '%7.1f' % (fpars['v2_dec'])
ResRec["anisotropy_v3_dec"] = '%7.1f' % (fpars['v3_dec'])
ResRec["anisotropy_v1_inc"] = '%7.1f' % (fpars['v1_inc'])
ResRec["anisotropy_v2_inc"] = '%7.1f' % (fpars['v2_inc'])
ResRec["anisotropy_v3_inc"] = '%7.1f' % (fpars['v3_inc'])
ResRec["anisotropy_t1"] = '%10.8f' % (fpars['t1'])
ResRec["anisotropy_t2"] = '%10.8f' % (fpars['t2'])
ResRec["anisotropy_t3"] = '%10.8f' % (fpars['t3'])
ResRec["anisotropy_ftest"] = '%10.3f' % (fpars['F'])
ResRec["anisotropy_ftest12"] = '%10.3f' % (fpars['F12'])
ResRec["anisotropy_ftest23"] = '%10.3f' % (fpars['F23'])
ResRec["result_description"] = 'F_crit: ' + fpars[
'F_crit'] + '; F12,F23_crit: ' + fpars['F12_crit']
ResRec['anisotropy_type'] = pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss) > 1:
if pmagplotlib.isServer:
title = "LO:_" + ResRec[
'er_location_names'] + '_SI:_' + site + '_SA:__SP:__CO:_' + crd
else:
title = ResRec['er_location_names']
if site:
title += "_{}".format(site)
title += '_{}'.format(crd)
ResRec['er_location_names'] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec,
ipar, title, iplot, comp, vec,
Dir, nb)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
ResRec['er_location_names'] = pmag.makelist(Locs)
if plots == 1:
save(ANIS, fmt, title)
ResRec = {}
ResRec['er_citation_names'] = pmag.makelist(Cits)
ResRec['er_location_names'] = pmag.makelist(Locs)
ResRec['er_site_names'] = pmag.makelist(Sites)
ResRec['er_sample_names'] = pmag.makelist(Samples)
ResRec['er_specimen_names'] = pmag.makelist(Specimens)
ResRec['rmag_result_name'] = pmag.makelist(
Sites) + ":" + pmag.makelist(anitypes)
ResRec['anisotropy_type'] = pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
if isite == "0":
ResRec[
'result_description'] = "Study average using coordinate system: " + CS
if isite == "1":
ResRec[
'result_description'] = "Site average using coordinate system: " + CS
if hpars != [] and ihext == 1:
HextRec = {}
for key in ResRec.keys():
HextRec[key] = ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = '%7.1f' % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = '%7.1f' % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = '%7.1f' % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = '%7.1f' % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = '%7.1f' % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = '%7.1f' % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = '%10.8f' % (hpars["t1"])
HextRec["anisotropy_t2"] = '%10.8f' % (hpars["t2"])
HextRec["anisotropy_t3"] = '%10.8f' % (hpars["t3"])
HextRec["anisotropy_hext_F"] = '%7.1f ' % (hpars["F"])
HextRec["anisotropy_hext_F12"] = '%7.1f ' % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = '%7.1f ' % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
hpars["v2_inc"])
HextRec["magic_method_codes"] = 'LP-AN:AE-H'
if verbose:
print("Hext Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
)
print(HextRec["anisotropy_t1"],
HextRec["anisotropy_v1_dec"],
HextRec["anisotropy_v1_inc"],
HextRec["anisotropy_v1_eta_semi_angle"],
HextRec["anisotropy_v1_eta_dec"],
HextRec["anisotropy_v1_eta_inc"],
HextRec["anisotropy_v1_zeta_semi_angle"],
HextRec["anisotropy_v1_zeta_dec"],
HextRec["anisotropy_v1_zeta_inc"])
print(HextRec["anisotropy_t2"],
HextRec["anisotropy_v2_dec"],
HextRec["anisotropy_v2_inc"],
HextRec["anisotropy_v2_eta_semi_angle"],
HextRec["anisotropy_v2_eta_dec"],
HextRec["anisotropy_v2_eta_inc"],
HextRec["anisotropy_v2_zeta_semi_angle"],
HextRec["anisotropy_v2_zeta_dec"],
HextRec["anisotropy_v2_zeta_inc"])
print(HextRec["anisotropy_t3"],
HextRec["anisotropy_v3_dec"],
HextRec["anisotropy_v3_inc"],
HextRec["anisotropy_v3_eta_semi_angle"],
HextRec["anisotropy_v3_eta_dec"],
HextRec["anisotropy_v3_eta_inc"],
HextRec["anisotropy_v3_zeta_semi_angle"],
HextRec["anisotropy_v3_zeta_dec"],
HextRec["anisotropy_v3_zeta_inc"])
HextRec['magic_software_packages'] = version_num
ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
for key in ResRec.keys():
BootRec[key] = ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = '%7.1f' % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = '%7.1f' % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = '%7.1f' % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = '%7.1f' % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = '%7.1f' % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = '%7.1f' % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = '%10.8f' % (bpars["t1"])
BootRec["anisotropy_t2"] = '%10.8f' % (bpars["t2"])
BootRec["anisotropy_t3"] = '%10.8f' % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (
bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (
bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (
bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (
bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (
bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (
bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ''
BootRec["anisotropy_hext_F12"] = ''
BootRec["anisotropy_hext_F23"] = ''
BootRec[
"magic_method_codes"] = 'LP-AN:AE-H:AE-BS' # regular bootstrap
if ipar == 1:
BootRec[
"magic_method_codes"] = 'LP-AN:AE-H:AE-BS-P' # parametric bootstrap
if verbose:
print("Boostrap Statistics: ")
print(
" tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
)
print(BootRec["anisotropy_t1"],
BootRec["anisotropy_v1_dec"],
BootRec["anisotropy_v1_inc"],
BootRec["anisotropy_v1_eta_semi_angle"],
BootRec["anisotropy_v1_eta_dec"],
BootRec["anisotropy_v1_eta_inc"],
BootRec["anisotropy_v1_zeta_semi_angle"],
BootRec["anisotropy_v1_zeta_dec"],
BootRec["anisotropy_v1_zeta_inc"])
print(BootRec["anisotropy_t2"],
BootRec["anisotropy_v2_dec"],
BootRec["anisotropy_v2_inc"],
BootRec["anisotropy_v2_eta_semi_angle"],
BootRec["anisotropy_v2_eta_dec"],
BootRec["anisotropy_v2_eta_inc"],
BootRec["anisotropy_v2_zeta_semi_angle"],
BootRec["anisotropy_v2_zeta_dec"],
BootRec["anisotropy_v2_zeta_inc"])
print(BootRec["anisotropy_t3"],
BootRec["anisotropy_v3_dec"],
BootRec["anisotropy_v3_inc"],
BootRec["anisotropy_v3_eta_semi_angle"],
BootRec["anisotropy_v3_eta_dec"],
BootRec["anisotropy_v3_eta_inc"],
BootRec["anisotropy_v3_zeta_semi_angle"],
BootRec["anisotropy_v3_zeta_dec"],
BootRec["anisotropy_v3_zeta_inc"])
BootRec['magic_software_packages'] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1: print("compare with [d]irection ")
print(
" plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
)
if isite == 1:
print(" [p]revious, [s]ite, [q]uit, <return> for next ")
ans = input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = input("Do Hext Statistics 1/[0]: ")
if e == "1": ihext = 1
e = input("Suppress bootstrap 1/[0]: ")
if e == "1": iboot = 0
if iboot == 1:
e = input("Parametric bootstrap 1/[0]: ")
if e == "1": ipar = 1
e = input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1": ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS['tcdf'] = 3
pmagplotlib.plot_init(ANIS['tcdf'], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp,
vec, Dir, nb)
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print("Current Coordinate system is: ")
if CS == '-1': print(" Specimen")
if CS == '0': print(" Geographic")
if CS == '100': print(" Tilt corrected")
key = input(
" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected "
)
if key == 's': CS = '-1'
if key == 'g': CS = '0'
if key == 't': CS = '100'
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = '-1'
if CS == '-1': crd = 's'
if CS == '0': crd = 'g'
if CS == '100': crd = 't'
print(
"desired coordinate system not available, using available: ",
crd)
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print("Good bye ")
sys.exit()
if ans == 'd':
if initcdf == 0:
initcdf = 1
ANIS['vxcdf'], ANIS['vycdf'], ANIS['vzcdf'] = 4, 5, 6
pmagplotlib.plot_init(ANIS['vxcdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vycdf'], 5, 5)
pmagplotlib.plot_init(ANIS['vzcdf'], 5, 5)
Dir, comp = [], 1
print("""
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction""")
con = 1
while con == 1:
try:
vdi = input("Vi D I: ").split()
vec = int(vdi[0]) - 1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print(" Incorrect entry, try again ")
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp,
vec, Dir, nb)
Dir, comp = [], 0
if ans == 'g':
con, cnt = 1, 0
while con == 1:
try:
print(
" Input: input pole to great circle ( D I) to plot a great circle: "
)
di = input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print(
" enter the dec and inc of the pole on one line "
)
else:
print(
"ummm - you are doing something wrong - i give up"
)
sys.exit()
pmagplotlib.plotC(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0: pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print(site, " not found, but this was: ")
print(tmplist)
site = input('Select one or try again\n ')
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
if pmagplotlib.isServer: # use server plot naming convention
title = "LO:_" + locs + '_SI:__' + '_SA:__SP:__CO:_' + crd
else: # use more readable plot naming convention
title = "{}_{}".format(locs, crd)
save(ANIS, fmt, title)
goon = 0
else:
if verbose: print('skipping plot - not enough data points')
k += 1
# put rmag_results stuff here
if len(ResRecs) > 0:
ResOut, keylist = pmag.fillkeys(ResRecs)
pmag.magic_write(outfile, ResOut, 'rmag_results')
if verbose:
print(" Good bye ")
def main():
"""
NAME
thellier_magic.py
DESCRIPTION
plots Thellier-Thellier, allowing interactive setting of bounds
and customizing of selection criteria. Saves and reads interpretations
from a pmag_specimen formatted table, default: thellier_specimens.txt
SYNTAX
thellier_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set magic_measurements input file
-fsp PRIOR, set pmag_specimen prior interpretations file
-fan ANIS, set rmag_anisotropy file for doing the anisotropy corrections
-fcr CRIT, set criteria file for grading.
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (default format)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds adn quits
-b BEG END: sets bounds for calculation
BEG: starting step for slope calculation
END: ending step for slope calculation
-z use only z component difference for pTRM calculation
DEFAULTS
MEAS: magic_measurements.txt
REDO: thellier_redo
CRIT: NONE
PRIOR: NONE
OUTPUT
figures:
ALL: numbers refer to temperature steps in command line window
1) Arai plot: closed circles are zero-field first/infield
open circles are infield first/zero-field
triangles are pTRM checks
squares are pTRM tail checks
VDS is vector difference sum
diamonds are bounds for interpretation
2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes
X rotated to NRM direction
3) (De/Re)Magnetization diagram:
circles are NRM remaining
squares are pTRM gained
4) equal area projections:
green triangles are pTRM gained direction
red (purple) circles are lower(upper) hemisphere of ZI step directions
blue (cyan) squares are lower(upper) hemisphere IZ step directions
5) Optional: TRM acquisition
6) Optional: TDS normalization
command line window:
list is: temperature step numbers, temperatures (C), Dec, Inc, Int (units of magic_measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates .svg format files with specimen_name, plot type as name
"""
#
# initializations
#
meas_file, critout, inspec = "magic_measurements.txt", "", "thellier_specimens.txt"
first = 1
inlt = 0
version_num = pmag.get_version()
TDinit, Tinit, field, first_save = 0, 0, -1, 1
user, comment, AniSpec, locname = "", '', "", ""
ans, specimen, recnum, start, end = 0, 0, 0, 0, 0
plots, pmag_out, samp_file, style = 0, "", "", "svg"
verbose = pmagplotlib.verbose
fmt = '.' + style
#
# default acceptance criteria
#
accept = pmag.default_criteria(0)[0] # set the default criteria
#
# parse command line options
#
Zdiff, anis = 0, 0
spc, BEG, END = "", "", ""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind + 1]
if '-fsp' in sys.argv:
ind = sys.argv.index('-fsp')
inspec = sys.argv[ind + 1]
if '-fan' in sys.argv:
ind = sys.argv.index('-fan')
anisfile = sys.argv[ind + 1]
anis = 1
anis_data, file_type = pmag.magic_read(anisfile)
if verbose:
print("Anisotropy data read in from ", anisfile)
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = '.' + sys.argv[ind + 1]
if '-dpi' in sys.argv:
ind = sys.argv.index('-dpi')
dpi = '.' + sys.argv[ind + 1]
else:
dpi = 100
if '-sav' in sys.argv:
plots = 1
verbose = 0
if '-z' in sys.argv:
Zdiff = 1
if '-spc' in sys.argv:
ind = sys.argv.index('-spc')
spc = sys.argv[ind + 1]
if '-b' in sys.argv:
ind = sys.argv.index('-b')
BEG = int(sys.argv[ind + 1])
END = int(sys.argv[ind + 2])
if '-fcr' in sys.argv:
ind = sys.argv.index('-fcr')
critout = sys.argv[ind + 1]
crit_data, file_type = pmag.magic_read(critout)
if file_type != 'pmag_criteria':
if verbose:
print('bad pmag_criteria file, using no acceptance criteria')
accept = pmag.default_criteria(1)[0]
else:
if verbose:
print("Acceptance criteria read in from ", critout)
accept = {
'pmag_criteria_code': 'ACCEPTANCE',
'er_citation_names': 'This study'
}
for critrec in crit_data:
if 'sample_int_sigma_uT' in critrec.keys(
): # accommodate Shaar's new criterion
critrec['sample_int_sigma'] = '%10.3e' % (
eval(critrec['sample_int_sigma_uT']) * 1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key] != '':
accept[key] = critrec[key]
try:
open(inspec, 'rU')
PriorRecs, file_type = pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print(file_type)
print(file_type, inspec, " is not a valid pmag_specimens file ")
sys.exit()
for rec in PriorRecs:
if 'magic_software_packages' not in rec.keys():
rec['magic_software_packages'] = ""
except IOError:
PriorRecs = []
if verbose:
print("starting new specimen interpretation file: ", inspec)
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()
backup = 0
# define figure numbers for arai, zijderveld and
# de-,re-magization diagrams
AZD = {}
AZD['deremag'], AZD['zijd'], AZD['arai'], AZD['eqarea'] = 1, 2, 3, 4
pmagplotlib.plot_init(AZD['arai'], 5, 5)
pmagplotlib.plot_init(AZD['zijd'], 5, 5)
pmagplotlib.plot_init(AZD['deremag'], 5, 5)
pmagplotlib.plot_init(AZD['eqarea'], 5, 5)
#
#
#
# get list of unique specimen names
#
CurrRec = []
sids = pmag.get_specs(meas_data)
# get plots for specimen s - default is just to step through arai diagrams
#
if spc != "":
specimen = sids.index(spc)
while specimen < len(sids):
methcodes = []
if verbose:
print(sids[specimen], specimen + 1, 'of ', len(sids))
MeasRecs = []
s = sids[specimen]
datablock, trmblock, tdsrecs = [], [], []
PmagSpecRec = {}
if first == 0:
for key in keys:
# make sure all new records have same set of keys
PmagSpecRec[key] = ""
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["specimen_correction"] = 'u'
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"] == s:
MeasRecs.append(rec)
if "magic_method_codes" not in rec.keys():
rec["magic_method_codes"] = ""
methods = rec["magic_method_codes"].split(":")
meths = []
for meth in methods:
meths.append(meth.strip()) # take off annoying spaces
methods = ""
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:
methcodes.append(meth.strip())
methods = methods + meth + ":"
methods = methods[:-1]
rec["magic_method_codes"] = methods
if "LP-PI-TRM" in meths:
datablock.append(rec)
if "LP-TRM" in meths:
trmblock.append(rec)
if "LP-TRM-TD" in meths:
tdsrecs.append(rec)
if len(trmblock) > 2 and inspec != "":
if Tinit == 0:
Tinit = 1
AZD['TRM'] = 5
pmagplotlib.plot_init(AZD['TRM'], 5, 5)
elif Tinit == 1: # clear the TRM figure if not needed
pmagplotlib.clearFIG(AZD['TRM'])
if len(tdsrecs) > 2:
if TDinit == 0:
TDinit = 1
AZD['TDS'] = 6
pmagplotlib.plot_init(AZD['TDS'], 5, 5)
elif TDinit == 1: # clear the TDS figure if not needed
pmagplotlib.clearFIG(AZD['TDS'])
if len(datablock) < 4:
if backup == 0:
specimen += 1
if verbose:
print('skipping specimen - moving forward ', s)
else:
specimen -= 1
if verbose:
print('skipping specimen - moving backward ', s)
#
# collect info for the PmagSpecRec dictionary
#
else:
rec = datablock[0]
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'].replace('/', '-')
if "er_expedition_name" in rec.keys():
PmagSpecRec["er_expedition_name"] = rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = ""
PmagSpecRec["magic_instrument_codes"] = rec[
"magic_instrument_codes"]
PmagSpecRec["measurement_step_unit"] = "K"
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec[
"magic_experiment_name"]
meths = rec["magic_method_codes"].split()
# sort data into types
araiblock, field = pmag.sortarai(datablock, s, Zdiff)
first_Z = araiblock[0]
GammaChecks = araiblock[5]
if len(first_Z) < 3:
if backup == 0:
specimen += 1
if verbose:
print('skipping specimen - moving forward ', s)
else:
specimen -= 1
if verbose:
print('skipping specimen - moving backward ', s)
else:
backup = 0
zijdblock, units = pmag.find_dmag_rec(s, meas_data)
recnum = 0
if verbose:
print("index step Dec Inc Int Gamma")
for plotrec in zijdblock:
if GammaChecks != "":
gamma = ""
for g in GammaChecks:
if g[0] == plotrec[0] - 273:
gamma = g[1]
break
if gamma != "":
print('%i %i %7.1f %7.1f %8.3e %7.1f' %
(recnum, plotrec[0] - 273, plotrec[1],
plotrec[2], plotrec[3], gamma))
else:
print('%i %i %7.1f %7.1f %8.3e ' %
(recnum, plotrec[0] - 273, plotrec[1],
plotrec[2], plotrec[3]))
recnum += 1
pmagplotlib.plot_arai_zij(AZD, araiblock, zijdblock, s,
units[0])
if verbose:
pmagplotlib.draw_figs(AZD)
if len(tdsrecs) > 2: # a TDS experiment
tdsblock = [] # make a list for the TDS data
Mkeys = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measuruement_magn_mass'
]
mkey, k = "", 0
# find which type of intensity
while mkey == "" and k < len(Mkeys) - 1:
key = Mkeys[k]
if key in tdsrecs[0].keys() and tdsrecs[0][key] != "":
mkey = key
k += 1
if mkey == "":
break # get outta here
Tnorm = ""
for tdrec in tdsrecs:
meths = tdrec['magic_method_codes'].split(":")
for meth in meths:
# strip off potential nasty spaces
meth.replace(" ", "")
if 'LT-T-I' in meths and Tnorm == "": # found first total TRM
# normalize by total TRM
Tnorm = float(tdrec[mkey])
# put in the zero step
tdsblock.append([273, zijdblock[0][3] / Tnorm, 1.])
# found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock
if 'LT-T-Z' in meths and Tnorm != "":
step = float(tdrec['treatment_temp'])
Tint = ""
if mkey != "":
Tint = float(tdrec[mkey])
if Tint != "":
for zrec in zijdblock:
if zrec[0] == step: # found matching
tdsblock.append([
step, zrec[3] / Tnorm, Tint / Tnorm
])
break
if len(tdsblock) > 2:
pmagplotlib.plot_tds(AZD['TDS'], tdsblock,
s + ':LP-PI-TDS:')
if verbose:
pmagplotlib(draw_figs(AZD))
else:
print("Something wrong here")
if anis == 1: # look up anisotropy data for this specimen
AniSpec = ""
for aspec in anis_data:
if aspec["er_specimen_name"] == PmagSpecRec[
"er_specimen_name"]:
AniSpec = aspec
if verbose:
print('Found anisotropy record...')
break
if inspec != "":
if verbose:
print('Looking up saved interpretation....')
found = 0
for k in range(len(PriorRecs)):
try:
if PriorRecs[k]["er_specimen_name"] == s:
found = 1
CurrRec.append(PriorRecs[k])
for j in range(len(zijdblock)):
if float(zijdblock[j][0]) == float(
PriorRecs[k]
["measurement_step_min"]):
start = j
if float(zijdblock[j][0]) == float(
PriorRecs[k]
["measurement_step_max"]):
end = j
pars, errcode = pmag.PintPars(
datablock, araiblock, zijdblock, start,
end, accept)
pars['measurement_step_unit'] = "K"
pars['experiment_type'] = 'LP-PI-TRM'
# put in CurrRec, take out of PriorRecs
del PriorRecs[k]
if errcode != 1:
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * \
field*pars["specimen_b"]
pars["er_specimen_name"] = s
if verbose:
print('Saved interpretation: ')
pars, kill = pmag.scoreit(
pars, PmagSpecRec, accept, '', verbose)
pmagplotlib.plot_b(AZD, araiblock,
zijdblock, pars)
if verbose:
pmagplotlib.draw_figs(AZD)
if len(trmblock) > 2:
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(
float(
trec['treatment_dc_field'])
)
TRMs.append(
float(trec[
'measurement_magn_moment'])
)
# calculate best fit parameters through TRM acquisition data, and get new banc
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0)
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
# predicted NRM for this field
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1])
Mp.append(npred)
pmagplotlib.plot_trm(
AZD['TRM'], Bs, TRMs, Bp, Mp,
NLpars,
trec['magic_experiment_name'])
PmagSpecRec['specimen_int'] = NLpars[
'banc']
if verbose:
print('Banc= ',
float(NLpars['banc']) * 1e6)
pmagplotlib.draw_figs(AZD)
mpars = pmag.domean(
araiblock[1], start, end, 'DE-BFL')
if verbose:
print(
'pTRM direction= ',
'%7.1f' % (mpars['specimen_dec']),
' %7.1f' % (mpars['specimen_inc']),
' MAD:',
'%7.1f' % (mpars['specimen_mad']))
if AniSpec != "":
CpTRM = pmag.Dir_anis_corr([
mpars['specimen_dec'],
mpars['specimen_inc']
], AniSpec)
AniSpecRec = pmag.doaniscorr(
PmagSpecRec, AniSpec)
if verbose:
print(
'Anisotropy corrected TRM direction= ',
'%7.1f' % (CpTRM[0]),
' %7.1f' % (CpTRM[1]))
print(
'Anisotropy corrected intensity= ',
float(
AniSpecRec['specimen_int'])
* 1e6)
else:
print('error on specimen ', s)
except:
pass
if verbose and found == 0:
print(' None found :( ')
if spc != "":
if BEG != "":
pars, errcode = pmag.PintPars(datablock, araiblock,
zijdblock, BEG, END,
accept)
pars['measurement_step_unit'] = "K"
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
pars["er_specimen_name"] = s
pars['specimen_grade'] = '' # ungraded
pmagplotlib.plot_b(AZD, araiblock, zijdblock, pars)
if verbose:
pmagplotlib.draw_figs(AZD)
if len(trmblock) > 2:
if inlt == 0:
inlt = 1
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(
float(trec['measurement_magn_moment']))
# calculate best fit parameters through TRM acquisition data, and get new banc
NLpars = nlt.NLtrm(Bs, TRMs, best, blab, 0)
#
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
# predicted NRM for this field
npred = nlt.TRM(Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1])
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.save_plots(AZD, files, dpi=dpi)
sys.exit()
if verbose:
ans = 'b'
while ans != "":
print("""
s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
""")
ans = input('Return for next specimen \n')
if ans == "":
specimen += 1
if ans == "d":
save_redo(PriorRecs, inspec)
CurrRec = []
pmagplotlib.plot_arai_zij(AZD, araiblock,
zijdblock, s, units[0])
if verbose:
pmagplotlib.draw_figs(AZD)
if ans == 'a':
files = {}
for key in AZD.keys():
files[key] = "LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name'] + \
'_SA:_' + \
PmagSpecRec['er_sample_name'] + \
'_SP:_'+s+'_CO:_s_TY:_'+key+fmt
pmagplotlib.save_plots(AZD, files)
ans = ""
if ans == 'q':
print("Good bye")
sys.exit()
if ans == 'p':
specimen = specimen - 1
backup = 1
ans = ""
if ans == 's':
keepon = 1
spec = input(
'Enter desired specimen name (or first part there of): '
)
while keepon == 1:
try:
specimen = sids.index(spec)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if spec in sids[qq]:
tmplist.append(sids[qq])
print(specimen,
" not found, but this was: ")
print(tmplist)
spec = input('Select one or try again\n ')
ans = ""
if ans == 'b':
if end == 0 or end >= len(zijdblock):
end = len(zijdblock) - 1
GoOn = 0
while GoOn == 0:
answer = input(
'Enter index of first point for calculation: ['
+ str(start) + '] ')
try:
start = int(answer)
answer = input(
'Enter index of last point for calculation: ['
+ str(end) + '] ')
end = int(answer)
if start >= 0 and start < len(
zijdblock
) - 2 and end > 0 and end < len(
zijdblock) or start >= end:
GoOn = 1
else:
print("Bad endpoints - try again! ")
start, end = 0, len(zijdblock)
except ValueError:
print("Bad endpoints - try again! ")
start, end = 0, len(zijdblock)
s = sids[specimen]
pars, errcode = pmag.PintPars(
datablock, araiblock, zijdblock, start, end,
accept)
pars['measurement_step_unit'] = "K"
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
pars["er_specimen_name"] = s
pars, kill = pmag.scoreit(pars, PmagSpecRec,
accept, '', 0)
PmagSpecRec['specimen_scat'] = pars[
'specimen_scat']
PmagSpecRec['specimen_frac'] = '%5.3f' % (
pars['specimen_frac'])
PmagSpecRec['specimen_gmax'] = '%5.3f' % (
pars['specimen_gmax'])
PmagSpecRec["measurement_step_min"] = '%8.3e' % (
pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"] = '%8.3e' % (
pars["measurement_step_max"])
PmagSpecRec["measurement_step_unit"] = "K"
PmagSpecRec["specimen_int_n"] = '%i' % (
pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"] = '%8.3e' % (
pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"] = '%9.4e ' % (
pars["specimen_int"])
PmagSpecRec["specimen_b"] = '%5.3f ' % (
pars["specimen_b"])
PmagSpecRec["specimen_q"] = '%5.1f ' % (
pars["specimen_q"])
PmagSpecRec["specimen_f"] = '%5.3f ' % (
pars["specimen_f"])
PmagSpecRec["specimen_fvds"] = '%5.3f' % (
pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"] = '%5.3f' % (
pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"] = '%7.1f' % (
pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"] = '%7.1f' % (
pars["specimen_Z"])
PmagSpecRec["specimen_gamma"] = '%7.1f' % (
pars["specimen_gamma"])
PmagSpecRec["specimen_grade"] = pars[
"specimen_grade"]
if pars["method_codes"] != "":
tmpcodes = pars["method_codes"].split(":")
for t in tmpcodes:
if t.strip() not in methcodes:
methcodes.append(t.strip())
PmagSpecRec["specimen_dec"] = '%7.1f' % (
pars["specimen_dec"])
PmagSpecRec["specimen_inc"] = '%7.1f' % (
pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"] = '-1'
PmagSpecRec["specimen_direction_type"] = 'l'
# this is redundant, but helpful - won't be imported
PmagSpecRec["direction_type"] = 'l'
PmagSpecRec["specimen_int_dang"] = '%7.1f ' % (
pars["specimen_int_dang"])
PmagSpecRec["specimen_drats"] = '%7.1f ' % (
pars["specimen_drats"])
PmagSpecRec["specimen_drat"] = '%7.1f ' % (
pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"] = '%i ' % (
pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"] = '%6.4f ' % (
pars["specimen_rsc"])
PmagSpecRec["specimen_md"] = '%i ' % (int(
pars["specimen_md"]))
if PmagSpecRec["specimen_md"] == '-1':
PmagSpecRec["specimen_md"] = ""
PmagSpecRec["specimen_b_sigma"] = '%5.3f ' % (
pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:
methcodes.append("IE-TT")
methods = ""
for meth in methcodes:
methods = methods + meth + ":"
PmagSpecRec["magic_method_codes"] = methods[:-1]
PmagSpecRec["specimen_description"] = comment
PmagSpecRec[
"magic_software_packages"] = version_num
pmagplotlib.plot_arai_zij(AZD, araiblock,
zijdblock, s, units[0])
pmagplotlib.plot_b(AZD, araiblock, zijdblock, pars)
if verbose:
pmagplotlib.draw_figs(AZD)
if len(trmblock) > 2:
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(float(
trec['treatment_dc_field']))
TRMs.append(
float(trec['measurement_magn_moment']))
# calculate best fit parameters through TRM acquisition data, and get new banc
NLpars = nlt.NLtrm(Bs, TRMs, best, blab, 0)
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
# predicted NRM for this field
npred = nlt.TRM(Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1])
Mp.append(npred)
pmagplotlib.plot_trm(
AZD['TRM'], Bs, TRMs, Bp, Mp, NLpars,
trec['magic_experiment_name'])
if verbose:
print(
'Non-linear TRM corrected intensity= ',
float(NLpars['banc']) * 1e6)
if verbose:
pmagplotlib.draw_figs(AZD)
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
pars, kill = pmag.scoreit(pars, PmagSpecRec,
accept, '', verbose)
saveit = input(
"Save this interpretation? [y]/n \n")
if saveit != 'n':
# put back an interpretation
PriorRecs.append(PmagSpecRec)
specimen += 1
save_redo(PriorRecs, inspec)
ans = ""
elif plots == 1:
specimen += 1
if fmt != ".pmag":
files = {}
for key in AZD.keys():
files[key] = "LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_' + \
PmagSpecRec['er_sample_name'] + \
'_SP:_'+s+'_CO:_s_TY:_'+key+'_'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['deremag'] = 'DeReMag Plot'
titles['zijd'] = 'Zijderveld Plot'
titles['arai'] = 'Arai Plot'
AZD = pmagplotlib.add_borders(
AZD, titles, black, purple)
pmagplotlib.save_plots(AZD, files, dpi=dpi)
# pmagplotlib.combineFigs(s,files,3)
else: # save in pmag format
script = "grep " + s + " output.mag | thellier -mfsi"
script = script + ' %8.4e' % (field)
min = '%i' % ((pars["measurement_step_min"] - 273))
Max = '%i' % ((pars["measurement_step_max"] - 273))
script = script + " " + min + " " + Max
script = script + " |plotxy;cat mypost >>thellier.ps\n"
pltf.write(script)
pmag.domagicmag(outf, MeasRecs)
if len(CurrRec) > 0:
for rec in CurrRec:
PriorRecs.append(rec)
CurrRec = []
if plots != 1 and verbose:
ans = input(" Save last plot? 1/[0] ")
if ans == "1":
if fmt != ".pmag":
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.save_plots(AZD, files, dpi=dpi)
else:
print("\n Good bye\n")
sys.exit()
if len(CurrRec) > 0:
PriorRecs.append(CurrRec) # put back an interpretation
if len(PriorRecs) > 0:
save_redo(PriorRecs, inspec)
print('Updated interpretations saved in ', inspec)
if verbose:
print("Good bye")
def main():
"""
NAME
thellier_magic_redo.py
DESCRIPTION
Calculates paleointensity parameters for thellier-thellier type data using bounds
stored in the "redo" file
SYNTAX
thellier_magic_redo [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-fcr CRIT, set criteria for grading
-f IN: specify input file, default is magic_measurements.txt
-fre REDO: specify redo file, default is "thellier_redo"
-F OUT: specify output file, default is thellier_specimens.txt
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
-CR PERC TYPE: apply a blanket cooling rate correction if none supplied in the er_samples.txt file
PERC should be a percentage of original (say reduce to 90%)
TYPE should be one of the following:
EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs)
-ANI: perform anisotropy correction
-fsa SAMPFILE: er_samples.txt file with cooling rate correction information, default is NO CORRECTION
-Fcr CRout: specify pmag_specimen format file for cooling rate corrected data
-fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt
-Fac ACout: specify pmag_specimen format file for anisotropy corrected data
default is AC_specimens.txt
-fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
-Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
default is NLT_specimens.txt
-z use z component differenences for pTRM calculation
INPUT
a thellier_redo file is Specimen_name Tmin Tmax (where Tmin and Tmax are in Centigrade)
"""
dir_path = '.'
critout = ""
version_num = pmag.get_version()
field, first_save = -1, 1
spec, recnum, start, end = 0, 0, 0, 0
crfrac = 0
NltRecs, PmagSpecs, AniSpecRecs, NltSpecRecs, CRSpecs = [], [], [], [], []
meas_file, pmag_file, mk_file = "magic_measurements.txt", "thellier_specimens.txt", "thellier_redo"
anis_file = "rmag_anisotropy.txt"
anisout, nltout = "AC_specimens.txt", "NLT_specimens.txt"
crout = "CR_specimens.txt"
nlt_file = ""
samp_file = ""
comment, user = "", "unknown"
anis, nltrm = 0, 0
jackknife = 0 # maybe in future can do jackknife
args = sys.argv
Zdiff = 0
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = sys.argv[ind + 1]
if "-leg" in args:
comment = "Recalculated from original measurements; supercedes published results. "
cool = 0
if "-CR" in args:
cool = 1
ind = args.index("-CR")
crfrac = .01 * float(sys.argv[ind + 1])
crtype = 'DA-CR-' + sys.argv[ind + 2]
if "-Fcr" in args:
ind = args.index("-Fcr")
crout = sys.argv[ind + 1]
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
pmag_file = sys.argv[ind + 1]
if "-fre" in args:
ind = args.index("-fre")
mk_file = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + '/' + args[ind + 1]
Samps, file_type = pmag.magic_read(samp_file)
SampCRs = pmag.get_dictitem(
Samps, 'cooling_rate_corr', '',
'F') # get samples cooling rate corrections
cool = 1
if file_type != 'er_samples':
print 'not a valid er_samples.txt file'
sys.exit()
#
#
if "-ANI" in args:
anis = 1
ind = args.index("-ANI")
if "-Fac" in args:
ind = args.index("-Fac")
anisout = args[ind + 1]
if "-fan" in args:
ind = args.index("-fan")
anis_file = args[ind + 1]
#
if "-NLT" in args:
if "-Fnl" in args:
ind = args.index("-Fnl")
nltout = args[ind + 1]
if "-fnl" in args:
ind = args.index("-fnl")
nlt_file = args[ind + 1]
if "-z" in args: Zdiff = 1
if '-fcr' in sys.argv:
ind = args.index("-fcr")
critout = sys.argv[ind + 1]
#
# start reading in data:
#
meas_file = dir_path + "/" + meas_file
mk_file = dir_path + "/" + mk_file
accept = pmag.default_criteria(1)[0] # set criteria to none
if critout != "":
critout = dir_path + "/" + critout
crit_data, file_type = pmag.magic_read(critout)
if file_type != 'pmag_criteria':
print 'bad pmag_criteria file, using no acceptance criteria'
print "Acceptance criteria read in from ", critout
for critrec in crit_data:
if 'sample_int_sigma_uT' in critrec.keys(
): # accommodate Shaar's new criterion
critrec['sample_int_sigma'] = '%10.3e' % (
eval(critrec['sample_int_sigma_uT']) * 1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key] != '':
accept[key] = critrec[key]
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()
try:
mk_f = open(mk_file, 'rU')
except:
print "Bad redo file"
sys.exit()
mkspec = []
speclist = []
for line in mk_f.readlines():
tmp = line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if anis == 1:
anis_file = dir_path + "/" + anis_file
anis_data, file_type = pmag.magic_read(anis_file)
if file_type != 'rmag_anisotropy':
print file_type
print file_type, "This is not a valid rmag_anisotropy file "
sys.exit()
if nlt_file == "":
nlt_data = pmag.get_dictitem(
meas_data, 'magic_method_codes', 'LP-TRM',
'has') # look for trm acquisition data in the meas_data file
else:
nlt_file = dir_path + "/" + nlt_file
nlt_data, file_type = pmag.magic_read(nlt_file)
if len(nlt_data) > 0:
nltrm = 1
#
# sort the specimen names and step through one by one
#
sids = pmag.get_specs(meas_data)
#
print 'Processing ', len(speclist), ' specimens - please wait '
while spec < len(speclist):
s = speclist[spec]
recnum = 0
datablock = []
PmagSpecRec = {}
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["er_citation_names"] = "This study"
PmagSpecRec["magic_software_packages"] = version_num
methcodes, inst_code = [], ""
#
# find the data from the meas_data file for this specimen
#
datablock = pmag.get_dictitem(meas_data, 'er_specimen_name', s, 'T')
datablock = pmag.get_dictitem(
datablock, 'magic_method_codes', 'LP-PI-TRM',
'has') #pick out the thellier experiment data
if len(datablock) > 0:
for rec in datablock:
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = "unknown"
#
# collect info for the PmagSpecRec dictionary
#
rec = datablock[0]
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["measurement_step_unit"] = "K"
PmagSpecRec["specimen_correction"] = 'u'
if "er_expedition_name" in rec.keys():
PmagSpecRec["er_expedition_name"] = rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():
PmagSpecRec["magic_instrument_codes"] = "unknown"
else:
PmagSpecRec["magic_instrument_codes"] = rec[
"magic_instrument_codes"]
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec[
"magic_experiment_name"]
meths = rec["magic_experiment_name"].split(":")
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:
methcodes.append(meth.strip())
#
# sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
#
araiblock, field = pmag.sortarai(datablock, s, Zdiff)
first_Z = araiblock[0]
first_I = araiblock[1]
ptrm_check = araiblock[2]
ptrm_tail = araiblock[3]
if len(first_I) < 3 or len(first_Z) < 4:
spec += 1
print 'skipping specimen ', s
else:
#
# get start, end
#
for redospec in mkspec:
if redospec[0] == s:
b, e = float(redospec[1]), float(redospec[2])
break
if e > float(first_Z[-1][0]): e = float(first_Z[-1][0])
for recnum in range(len(first_Z)):
if first_Z[recnum][0] == b: start = recnum
if first_Z[recnum][0] == e: end = recnum
nsteps = end - start
if nsteps > 2:
zijdblock, units = pmag.find_dmag_rec(s, meas_data)
pars, errcode = pmag.PintPars(datablock, araiblock,
zijdblock, start, end,
accept)
if 'specimen_scat' in pars.keys():
PmagSpecRec['specimen_scat'] = pars['specimen_scat']
if 'specimen_frac' in pars.keys():
PmagSpecRec['specimen_frac'] = '%5.3f' % (
pars['specimen_frac'])
if 'specimen_gmax' in pars.keys():
PmagSpecRec['specimen_gmax'] = '%5.3f' % (
pars['specimen_gmax'])
pars['measurement_step_unit'] = units
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
PmagSpecRec["measurement_step_min"] = '%8.3e' % (
pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"] = '%8.3e' % (
pars["measurement_step_max"])
PmagSpecRec["specimen_int_n"] = '%i' % (
pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"] = '%8.3e' % (
pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"] = '%9.4e ' % (
pars["specimen_int"])
PmagSpecRec["specimen_b"] = '%5.3f ' % (pars["specimen_b"])
PmagSpecRec["specimen_q"] = '%5.1f ' % (pars["specimen_q"])
PmagSpecRec["specimen_f"] = '%5.3f ' % (pars["specimen_f"])
PmagSpecRec["specimen_fvds"] = '%5.3f' % (
pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"] = '%5.3f' % (
pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"] = '%7.1f' % (
pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"] = '%7.1f' % (pars["specimen_Z"])
PmagSpecRec["specimen_gamma"] = '%7.1f' % (
pars["specimen_gamma"])
if pars["method_codes"] != "" and pars[
"method_codes"] not in methcodes:
methcodes.append(pars["method_codes"])
PmagSpecRec["specimen_dec"] = '%7.1f' % (
pars["specimen_dec"])
PmagSpecRec["specimen_inc"] = '%7.1f' % (
pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"] = '-1'
PmagSpecRec["specimen_direction_type"] = 'l'
PmagSpecRec[
"direction_type"] = 'l' # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"] = '%7.1f ' % (
pars["specimen_dang"])
PmagSpecRec["specimen_drats"] = '%7.1f ' % (
pars["specimen_drats"])
PmagSpecRec["specimen_drat"] = '%7.1f ' % (
pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"] = '%i ' % (
pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"] = '%6.4f ' % (
pars["specimen_rsc"])
PmagSpecRec["specimen_md"] = '%i ' % (int(
pars["specimen_md"]))
if PmagSpecRec["specimen_md"] == '-1':
PmagSpecRec["specimen_md"] = ""
PmagSpecRec["specimen_b_sigma"] = '%5.3f ' % (
pars["specimen_b_sigma"])
if "IE-TT" not in methcodes: methcodes.append("IE-TT")
methods = ""
for meth in methcodes:
methods = methods + meth + ":"
PmagSpecRec["magic_method_codes"] = methods.strip(':')
PmagSpecRec["magic_software_packages"] = version_num
PmagSpecRec["specimen_description"] = comment
if critout != "":
kill = pmag.grade(PmagSpecRec, accept, 'specimen_int')
if len(kill) > 0:
Grade = 'F' # fails
else:
Grade = 'A' # passes
PmagSpecRec["specimen_grade"] = Grade
else:
PmagSpecRec["specimen_grade"] = "" # not graded
if nltrm == 0 and anis == 0 and cool != 0: # apply cooling rate correction
SCR = pmag.get_dictitem(
SampCRs, 'er_sample_name',
PmagSpecRec['er_sample_name'],
'T') # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(PmagSpecRec, SCR, crfrac,
crtype)
if CrSpecRec['er_specimen_name'] != 'none':
CrSpecs.append(CrSpecRec)
PmagSpecs.append(PmagSpecRec)
NltSpecRec = ""
#
# check on non-linear TRM correction
#
if nltrm == 1:
#
# find the data from the nlt_data list for this specimen
#
TRMs, Bs = [], []
NltSpecRec = ""
NltRecs = pmag.get_dictitem(
nlt_data, 'er_specimen_name',
PmagSpecRec['er_specimen_name'], 'has'
) # fish out all the NLT data for this specimen
if len(NltRecs) > 2:
for NltRec in NltRecs:
Bs.append(float(NltRec['treatment_dc_field']))
TRMs.append(
float(NltRec['measurement_magn_moment']))
NLTpars = nlt.NLtrm(
Bs, TRMs, float(PmagSpecRec['specimen_int']),
float(PmagSpecRec['specimen_lab_field_dc']), 0)
if NLTpars['banc'] > 0:
NltSpecRec = {}
for key in PmagSpecRec.keys():
NltSpecRec[key] = PmagSpecRec[key]
NltSpecRec['specimen_int'] = '%9.4e' % (
NLTpars['banc'])
NltSpecRec['magic_method_codes'] = PmagSpecRec[
"magic_method_codes"] + ":DA-NL"
NltSpecRec["specimen_correction"] = 'c'
NltSpecRec['specimen_grade'] = PmagSpecRec[
'specimen_grade']
NltSpecRec[
"magic_software_packages"] = version_num
print NltSpecRec[
'er_specimen_name'], ' Banc= ', float(
NLTpars['banc']) * 1e6
if anis == 0 and cool != 0:
SCR = pmag.get_dictitem(
SampCRs, 'er_sample_name',
NltSpecRec['er_sample_name'], 'T'
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(
NltSpecRec, SCR, crfrac, crtype)
if CrSpecRec['er_specimen_name'] != 'none':
CrSpecs.append(CrSpecRec)
NltSpecRecs.append(NltSpecRec)
#
# check on anisotropy correction
if anis == 1:
if NltSpecRec != "":
Spc = NltSpecRec
else: # find uncorrected data
Spc = PmagSpecRec
AniSpecs = pmag.get_dictitem(
anis_data, 'er_specimen_name',
PmagSpecRec['er_specimen_name'], 'T')
if len(AniSpecs) > 0:
AniSpec = AniSpecs[0]
AniSpecRec = pmag.doaniscorr(Spc, AniSpec)
AniSpecRec['specimen_grade'] = PmagSpecRec[
'specimen_grade']
AniSpecRec[
"magic_instrument_codes"] = PmagSpecRec[
'magic_instrument_codes']
AniSpecRec["specimen_correction"] = 'c'
AniSpecRec[
"magic_software_packages"] = version_num
if cool != 0:
SCR = pmag.get_dictitem(
SampCRs, 'er_sample_name',
AniSpecRec['er_sample_name'], 'T'
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(
AniSpecRec, SCR, crfrac, crtype)
if CrSpecRec['er_specimen_name'] != 'none':
CrSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
elif anis == 1:
AniSpecs = pmag.get_dictitem(
anis_data, 'er_specimen_name',
PmagSpecRec['er_specimen_name'], 'T')
if len(AniSpecs) > 0:
AniSpec = AniSpecs[0]
AniSpecRec = pmag.doaniscorr(PmagSpecRec, AniSpec)
AniSpecRec['specimen_grade'] = PmagSpecRec[
'specimen_grade']
AniSpecRec["magic_instrument_codes"] = PmagSpecRec[
"magic_instrument_codes"]
AniSpecRec["specimen_correction"] = 'c'
AniSpecRec["magic_software_packages"] = version_num
if crfrac != 0:
CrSpecRec = {}
for key in AniSpecRec.keys():
CrSpecRec[key] = AniSpecRec[key]
inten = frac * float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"] = '%9.4e ' % (
inten
) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec[
'magic_method_codes'] + ':DA-CR-' + crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
spec += 1
else:
print "skipping ", s
spec += 1
pmag_file = dir_path + '/' + pmag_file
pmag.magic_write(pmag_file, PmagSpecs, 'pmag_specimens')
print 'uncorrected thellier data saved in: ', pmag_file
if anis == 1 and len(AniSpecRecs) > 0:
anisout = dir_path + '/' + anisout
pmag.magic_write(anisout, AniSpecRecs, 'pmag_specimens')
print 'anisotropy corrected data saved in: ', anisout
if nltrm == 1 and len(NltSpecRecs) > 0:
nltout = dir_path + '/' + nltout
pmag.magic_write(nltout, NltSpecRecs, 'pmag_specimens')
print 'non-linear TRM corrected data saved in: ', nltout
if crfrac != 0:
crout = dir_path + '/' + crout
pmag.magic_write(crout, CRSpecs, 'pmag_specimens')
print 'cooling rate corrected data saved in: ', crout
def main(command_line=True, **kwargs):
"""
NAME
old_iodp_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
old_iodp_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave=0
volume=2.5**3 #default volume is a 2.5cm cube
inst=""
samp_con,Z='5',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
version_num=pmag.get_version()
dir_path='.'
MagRecs=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-fsa' in args:
ind = args.index("-fsa")
samp_file = args[ind+1]
if samp_file[0]!='/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
except:
print samp_file,' not found: '
print ' download csv file and import to MagIC with iodp_samples_magic.py'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args:
noave=1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print "You must provide an IODP_jr6 format file"
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(os.path.join(input_dir_path, mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(magfile)
if not os.path.exists(samp_file):
print 'samp_file', samp_file
print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
#os.rename('temp.txt', mag_file)
#data = open(mag_file, 'rU').readlines()
data=pd.read_csv(temp, delim_whitespace=True,header=None)
os.remove(temp)
samples,filetype = pmag.magic_read(samp_file)
data.columns=['specname','step','negz','y','x','expon','sample_azimuth','sample_dip','sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['measurement_flag']='g'
data['measurement_standard']='u'
data['measurement_number']='1'
data['measurement_temp']='273'
data['er_location_name']=er_location_name
for rowNum, row in data.iterrows():
MagRec={}
spec_text_id=row['specname'].split('_')[1]
SampRecs=pmag.get_dictitem(samples,'er_sample_alternatives',spec_text_id,'has') # retrieve sample record for this specimen
if len(SampRecs)>0: # found one
MagRec['er_specimen_name']=SampRecs[0]['er_sample_name']
MagRec['er_sample_name']=MagRec['er_specimen_name']
MagRec['er_site_name']=MagRec['er_specimen_name']
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["treatment_ac_field"]='0'
volume=float(SampRecs[0]['sample_volume'])
moment=row['measurement_magn_volume'] * volume
MagRec["measurement_magn_moment"]=str(moment)
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]='%7.1f'%(row['measurement_dec'])
MagRec["measurement_inc"]='%7.1f'%(row['measurement_inc'])
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:3]=='ARM': #
meas_type="LT-AF-I"
treat=float(row['step'][3:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field
MagRec["measurement_description"]='Assumed DC field - actual unknown'
elif row['step'][0:3]=='IRM': #
meas_type="LT-IRM"
treat=float(row['step'][3:])
MagRec["treatment_dc_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
else:
print 'unknown treatment type for ',row
return False, 'unknown treatment type for ',row
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
else:
print 'sample name not found: ',row['specname']
MagOuts=pmag.measurements_methods(MagRecs,noave)
file_created, error_message = pmag.magic_write(meas_file,MagOuts,'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main():
"""
NAME
trmaq_magic.py
DESCTIPTION
does non-linear trm acquisisiton correction
SYNTAX
trmaq_magic.py [-h][-i][command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-f MFILE, sets magic_measurements input file
-ft TSPEC, sets thellier_specimens input file
-F OUT, sets output for non-linear TRM acquisition corrected data
DEFAULTS
MFILE: trmaq_measurements.txt
TSPEC: thellier_specimens.txt
OUT: NLT_specimens.txt
"""
meas_file='trmaq_measurements.txt'
tspec="thellier_specimens.txt"
output='NLT_specimens.txt'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-i' in sys.argv:
meas_file=raw_input("Input magic_measurements file name? [trmaq_measurements.txt] ")
if meas_file=="":meas_file="trmaq_measurements.txt"
tspec=raw_input(" thellier_specimens file name? [thellier_specimens.txt] ")
if tspec=="":tspec="thellier_specimens.txt"
output=raw_input("File for non-linear TRM adjusted specimen data: [NLTspecimens.txt] ")
if output=="":output="NLT_specimens.txt"
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-ft' in sys.argv:
ind=sys.argv.index('-ft')
tspec=sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
output=sys.argv[ind+1]
#
PLT={'aq':1}
pmagplotlib.plot_init(PLT['aq'],5,5)
#
# get name of file from command line
#
comment=""
#
#
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()
sids=pmag.get_specs(meas_data)
specimen=0
#
# read in thellier_specimen data
#
nrm,file_type=pmag.magic_read(tspec)
PmagSpecRecs=[]
while specimen < len(sids):
#
# find corresoponding paleointensity data for this specimen
#
s=sids[specimen]
blab,best="",""
for nrec in nrm: # pick out the Banc data for this spec
if nrec["er_specimen_name"]==s:
blab=float(nrec["specimen_lab_field_dc"])
best=float(nrec["specimen_int"])
TrmRec=nrec
break
if blab=="":
print "skipping ",s," : no best "
specimen+=1
else:
print sids[specimen],specimen+1, 'of ', len(sids),'Best = ',best*1e6
MeasRecs=[]
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"]==s:
meths=rec["magic_method_codes"].split(":")
methcodes=[]
for meth in meths:
methcodes.append(meth.strip())
if "LP-TRM" in methcodes: MeasRecs.append(rec)
if len(MeasRecs) <2:
specimen+=1
print 'skipping specimen - no trm acquisition data ', s
#
# collect info for the PmagSpecRec dictionary
#
else:
TRMs,Bs=[],[]
for rec in MeasRecs:
Bs.append(float(rec['treatment_dc_field']))
TRMs.append(float(rec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(PLT['aq'],Bs,TRMs,Bp,Mp,NLpars,rec['magic_experiment_name'])
pmagplotlib.drawFIGS(PLT)
print 'Banc= ',float(NLpars['banc'])*1e6
trmTC={}
for key in TrmRec.keys():
trmTC[key]=TrmRec[key] # copy of info from thellier_specimens record
trmTC['specimen_int']='%8.3e'%(NLpars['banc'])
trmTC['magic_method_codes']=TrmRec["magic_method_codes"]+":DA-NL"
PmagSpecRecs.append(trmTC)
ans=raw_input("Return for next specimen, s[a]ve plot ")
if ans=='a':
Name={'aq':rec['er_specimen_name']+'_TRM.svg'}
pmagplotlib.saveP(PLT,Name)
specimen+=1
pmag.magic_write(output,PmagSpecRecs,'pmag_specimens')
def main():
"""
NAME
aarm_magic.py
DESCRIPTION
Converts AARM data to best-fit tensor (6 elements plus sigma)
Original program ARMcrunch written to accomodate ARM anisotropy data
collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the
off-axis remanence terms to construct the tensor. A better way to
do the anisotropy of ARMs is to use 9,12 or 15 measurements in
the Hext rotational scheme.
SYNTAX
aarm_magic.py [-h][command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f FILE: specify input file, default is aarm_measurements.txt
-crd [s,g,t] specify coordinate system, requires er_samples.txt file
-fsa FILE: specify er_samples.txt file, default is er_samples.txt
-Fa FILE: specify anisotropy output file, default is arm_anisotropy.txt
-Fr FILE: specify results output file, default is aarm_results.txt
INPUT
Input for the present program is a series of baseline, ARM pairs.
The baseline should be the AF demagnetized state (3 axis demag is
preferable) for the following ARM acquisition. The order of the
measurements is:
positions 1,2,3, 6,7,8, 11,12,13 (for 9 positions)
positions 1,2,3,4, 6,7,8,9, 11,12,13,14 (for 12 positions)
positions 1-15 (for 15 positions)
"""
# initialize some parameters
args = sys.argv
user = ""
meas_file = "aarm_measurements.txt"
samp_file = "er_samples.txt"
rmag_anis = "arm_anisotropy.txt"
rmag_res = "aarm_results.txt"
dir_path = '.'
#
# get name of file from command line
#
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = sys.argv[ind + 1]
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
coord = '-1'
if "-crd" in sys.argv:
ind = sys.argv.index("-crd")
coord = sys.argv[ind + 1]
if coord == 's': coord = '-1'
if coord == 'g': coord = '0'
if coord == 't': coord = '100'
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = sys.argv[ind + 1]
if "-Fa" in args:
ind = args.index("-Fa")
rmag_anis = args[ind + 1]
if "-Fr" in args:
ind = args.index("-Fr")
rmag_res = args[ind + 1]
meas_file = dir_path + '/' + meas_file
samp_file = dir_path + '/' + samp_file
rmag_anis = dir_path + '/' + rmag_anis
rmag_res = dir_path + '/' + rmag_res
# read in data
meas_data, file_type = pmag.magic_read(meas_file)
meas_data = pmag.get_dictitem(meas_data, 'magic_method_codes', 'LP-AN-ARM',
'has')
if file_type != 'magic_measurements':
print file_type
print file_type, "This is not a valid magic_measurements file "
sys.exit()
if coord != '-1': # need to read in sample data
samp_data, file_type = pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print file_type, "This is not a valid er_samples file "
print "Only specimen coordinates will be calculated"
coord = '-1'
#
# sort the specimen names
#
ssort = []
for rec in meas_data:
spec = rec["er_specimen_name"]
if spec not in ssort: ssort.append(spec)
if len(ssort) > 1:
sids = sorted(ssort)
else:
sids = ssort
#
# work on each specimen
#
specimen = 0
RmagSpecRecs, RmagResRecs = [], []
while specimen < len(sids):
s = sids[specimen]
data = []
RmagSpecRec = {}
RmagResRec = {}
method_codes = []
#
# find the data from the meas_data file for this sample
#
data = pmag.get_dictitem(meas_data, 'er_specimen_name', s, 'T')
#
# find out the number of measurements (9, 12 or 15)
#
npos = len(data) / 2
if npos == 9:
#
# get dec, inc, int and convert to x,y,z
#
B, H, tmpH = pmag.designAARM(
npos) # B matrix made from design matrix for positions
X = []
for rec in data:
Dir = []
Dir.append(float(rec["measurement_dec"]))
Dir.append(float(rec["measurement_inc"]))
Dir.append(float(rec["measurement_magn_moment"]))
X.append(pmag.dir2cart(Dir))
#
# subtract baseline and put in a work array
#
work = numpy.zeros((npos, 3), 'f')
for i in range(npos):
for j in range(3):
work[i][j] = X[2 * i + 1][j] - X[2 * i][j]
#
# calculate tensor elements
# first put ARM components in w vector
#
w = numpy.zeros((npos * 3), 'f')
index = 0
for i in range(npos):
for j in range(3):
w[index] = work[i][j]
index += 1
s = numpy.zeros((6), 'f') # initialize the s matrix
for i in range(6):
for j in range(len(w)):
s[i] += B[i][j] * w[j]
trace = s[0] + s[1] + s[2] # normalize by the trace
for i in range(6):
s[i] = s[i] / trace
a = pmag.s2a(s)
#------------------------------------------------------------
# Calculating dels is different than in the Kappabridge
# routine. Use trace normalized tensor (a) and the applied
# unit field directions (tmpH) to generate model X,Y,Z
# components. Then compare these with the measured values.
#------------------------------------------------------------
S = 0.
comp = numpy.zeros((npos * 3), 'f')
for i in range(npos):
for j in range(3):
index = i * 3 + j
compare = a[j][0] * tmpH[i][0] + a[j][1] * tmpH[i][1] + a[
j][2] * tmpH[i][2]
comp[index] = compare
for i in range(npos * 3):
d = w[i] / trace - comp[i] # del values
S += d * d
nf = float(npos * 3 - 6) # number of degrees of freedom
if S > 0:
sigma = numpy.sqrt(S / nf)
else:
sigma = 0
RmagSpecRec["rmag_anisotropy_name"] = data[0]["er_specimen_name"]
RmagSpecRec["er_location_name"] = data[0]["er_location_name"]
RmagSpecRec["er_specimen_name"] = data[0]["er_specimen_name"]
RmagSpecRec["er_sample_name"] = data[0]["er_sample_name"]
RmagSpecRec["er_site_name"] = data[0]["er_site_name"]
RmagSpecRec["magic_experiment_names"] = RmagSpecRec[
"rmag_anisotropy_name"] + ":AARM"
RmagSpecRec["er_citation_names"] = "This study"
RmagResRec[
"rmag_result_name"] = data[0]["er_specimen_name"] + ":AARM"
RmagResRec["er_location_names"] = data[0]["er_location_name"]
RmagResRec["er_specimen_names"] = data[0]["er_specimen_name"]
RmagResRec["er_sample_names"] = data[0]["er_sample_name"]
RmagResRec["er_site_names"] = data[0]["er_site_name"]
RmagResRec["magic_experiment_names"] = RmagSpecRec[
"rmag_anisotropy_name"] + ":AARM"
RmagResRec["er_citation_names"] = "This study"
if "magic_instrument_codes" in data[0].keys():
RmagSpecRec["magic_instrument_codes"] = data[0][
"magic_instrument_codes"]
else:
RmagSpecRec["magic_instrument_codes"] = ""
RmagSpecRec["anisotropy_type"] = "AARM"
RmagSpecRec[
"anisotropy_description"] = "Hext statistics adapted to AARM"
if coord != '-1': # need to rotate s
# set orientation priorities
SO_methods = []
for rec in samp_data:
if "magic_method_codes" not in rec:
rec['magic_method_codes'] = 'SO-NO'
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())
SO_priorities = pmag.set_priorities(SO_methods, 0)
# continue here
redo, p = 1, 0
if len(SO_methods) <= 1:
az_type = SO_methods[0]
orient = pmag.find_samp_rec(RmagSpecRec["er_sample_name"],
samp_data, az_type)
if orient["sample_azimuth"] != "":
method_codes.append(az_type)
redo = 0
while redo == 1:
if p >= len(SO_priorities):
print "no orientation data for ", s
orient["sample_azimuth"] = ""
orient["sample_dip"] = ""
method_codes.append("SO-NO")
redo = 0
else:
az_type = SO_methods[SO_methods.index(
SO_priorities[p])]
orient = pmag.find_samp_rec(
PmagSpecRec["er_sample_name"], samp_data, az_type)
if orient["sample_azimuth"] != "":
method_codes.append(az_type)
redo = 0
p += 1
az, pl = orient['sample_azimuth'], orient['sample_dip']
s = pmag.dosgeo(s, az, pl) # rotate to geographic coordinates
if coord == '100':
sampe_bed_dir, sample_bed_dip = orient[
'sample_bed_dip_direction'], orient['sample_bed_dip']
s = pmag.dostilt(
s, bed_dir,
bed_dip) # rotate to geographic coordinates
hpars = pmag.dohext(nf, sigma, s)
#
# prepare for output
#
RmagSpecRec["anisotropy_s1"] = '%8.6f' % (s[0])
RmagSpecRec["anisotropy_s2"] = '%8.6f' % (s[1])
RmagSpecRec["anisotropy_s3"] = '%8.6f' % (s[2])
RmagSpecRec["anisotropy_s4"] = '%8.6f' % (s[3])
RmagSpecRec["anisotropy_s5"] = '%8.6f' % (s[4])
RmagSpecRec["anisotropy_s6"] = '%8.6f' % (s[5])
RmagSpecRec["anisotropy_mean"] = '%8.3e' % (trace / 3)
RmagSpecRec["anisotropy_sigma"] = '%8.6f' % (sigma)
RmagSpecRec["anisotropy_unit"] = "Am^2"
RmagSpecRec["anisotropy_n"] = '%i' % (npos)
RmagSpecRec["anisotropy_tilt_correction"] = coord
RmagSpecRec["anisotropy_F"] = '%7.1f ' % (
hpars["F"]
) # used by thellier_gui - must be taken out for uploading
RmagSpecRec["anisotropy_F_crit"] = hpars[
"F_crit"] # used by thellier_gui - must be taken out for uploading
RmagResRec["anisotropy_t1"] = '%8.6f ' % (hpars["t1"])
RmagResRec["anisotropy_t2"] = '%8.6f ' % (hpars["t2"])
RmagResRec["anisotropy_t3"] = '%8.6f ' % (hpars["t3"])
RmagResRec["anisotropy_v1_dec"] = '%7.1f ' % (hpars["v1_dec"])
RmagResRec["anisotropy_v2_dec"] = '%7.1f ' % (hpars["v2_dec"])
RmagResRec["anisotropy_v3_dec"] = '%7.1f ' % (hpars["v3_dec"])
RmagResRec["anisotropy_v1_inc"] = '%7.1f ' % (hpars["v1_inc"])
RmagResRec["anisotropy_v2_inc"] = '%7.1f ' % (hpars["v2_inc"])
RmagResRec["anisotropy_v3_inc"] = '%7.1f ' % (hpars["v3_inc"])
RmagResRec["anisotropy_ftest"] = '%7.1f ' % (hpars["F"])
RmagResRec["anisotropy_ftest12"] = '%7.1f ' % (hpars["F12"])
RmagResRec["anisotropy_ftest23"] = '%7.1f ' % (hpars["F23"])
RmagResRec["result_description"] = 'Critical F: ' + hpars[
"F_crit"] + ';Critical F12/F13: ' + hpars["F12_crit"]
if hpars["e12"] > hpars["e13"]:
RmagResRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
hpars['e12'])
RmagResRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
hpars['v2_dec'])
RmagResRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
hpars['v2_inc'])
RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
hpars['e13'])
RmagResRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (
hpars['v3_dec'])
RmagResRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (
hpars['v3_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (
hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (
hpars['v1_inc'])
else:
RmagResRec["anisotropy_v1_zeta_semi_angle"] = '%7.1f ' % (
hpars['e13'])
RmagResRec["anisotropy_v1_zeta_dec"] = '%7.1f ' % (
hpars['v3_dec'])
RmagResRec["anisotropy_v1_zeta_inc"] = '%7.1f ' % (
hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"] = '%7.1f ' % (
hpars['e12'])
RmagResRec["anisotropy_v1_eta_dec"] = '%7.1f ' % (
hpars['v2_dec'])
RmagResRec["anisotropy_v1_eta_inc"] = '%7.1f ' % (
hpars['v2_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (
hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (
hpars['v1_inc'])
if hpars["e23"] > hpars['e12']:
RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
hpars['e23'])
RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
hpars['v3_dec'])
RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
hpars['e23'])
RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
hpars['v2_dec'])
RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
hpars['v2_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (
hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (
hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (
hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (
hpars['v1_inc'])
else:
RmagResRec["anisotropy_v2_zeta_semi_angle"] = '%7.1f ' % (
hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"] = '%7.1f ' % (
hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"] = '%7.1f ' % (
hpars['v1_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"] = '%7.1f ' % (
hpars['e23'])
RmagResRec["anisotropy_v3_eta_dec"] = '%7.1f ' % (
hpars['v2_dec'])
RmagResRec["anisotropy_v3_eta_inc"] = '%7.1f ' % (
hpars['v2_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"] = '%7.1f ' % (
hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"] = '%7.1f ' % (
hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"] = '%7.1f ' % (
hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"] = '%7.1f ' % (
hpars['e23'])
RmagResRec["anisotropy_v2_eta_dec"] = '%7.1f ' % (
hpars['v3_dec'])
RmagResRec["anisotropy_v2_eta_inc"] = '%7.1f ' % (
hpars['v3_inc'])
RmagResRec["tilt_correction"] = '-1'
RmagResRec["anisotropy_type"] = 'AARM'
RmagResRec["magic_method_codes"] = 'LP-AN-ARM:AE-H'
RmagSpecRec["magic_method_codes"] = 'LP-AN-ARM:AE-H'
RmagResRec["magic_software_packages"] = pmag.get_version()
RmagSpecRec["magic_software_packages"] = pmag.get_version()
specimen += 1
RmagSpecRecs.append(RmagSpecRec)
RmagResRecs.append(RmagResRec)
else:
print 'skipping specimen ', s, ' only 9 positions supported', '; this has ', npos
specimen += 1
if rmag_anis == "": rmag_anis = "rmag_anisotropy.txt"
pmag.magic_write(rmag_anis, RmagSpecRecs, 'rmag_anisotropy')
print "specimen tensor elements stored in ", rmag_anis
if rmag_res == "": rmag_res = "rmag_results.txt"
pmag.magic_write(rmag_res, RmagResRecs, 'rmag_results')
print "specimen statistics and eigenparameters stored in ", rmag_res
def main():
"""
NAME
dayplot_magic.py
DESCRIPTION
makes 'day plots' (Day et al. 1977) and squareness/coercivity,
plots 'linear mixing' curve from Dunlop and Carter-Stiglitz (2006).
squareness coercivity of remanence (Neel, 1955) plots after
Tauxe et al. (2002)
SYNTAX
dayplot_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input hysteresis file, default is rmag_hysteresis.txt
-fr: specify input remanence file, default is rmag_remanence.txt
-fmt [svg,png,jpg] format for output plots
-sav saves plots and quits quietly
-n label specimen names
"""
args=sys.argv
hyst_file,rem_file="rmag_hysteresis.txt","rmag_remanence.txt"
dir_path='.'
verbose=pmagplotlib.verbose
fmt='svg' # default file format
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-f' in args:
ind=args.index("-f")
hyst_file=args[ind+1]
if '-fr' in args:
ind=args.index("-fr")
rem_file=args[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:
plots=1
verbose=0
else: plots=0
if '-n' in sys.argv:
label=1
else:
label=0
hyst_file = os.path.realpath(os.path.join(dir_path, hyst_file))
rem_file = os.path.realpath(os.path.join(dir_path, rem_file))
#
# initialize some variables
# define figure numbers for Day,S-Bc,S-Bcr
DSC={}
DSC['day'],DSC['S-Bc'],DSC['S-Bcr'],DSC['bcr1-bcr2']=1,2,3,4
pmagplotlib.plot_init(DSC['day'],5,5)
pmagplotlib.plot_init(DSC['S-Bc'],5,5)
pmagplotlib.plot_init(DSC['S-Bcr'],5,5)
pmagplotlib.plot_init(DSC['bcr1-bcr2'],5,5)
#
#
hyst_data,file_type=pmag.magic_read(hyst_file)
rem_data,file_type=pmag.magic_read(rem_file)
#
S,BcrBc,Bcr2,Bc,hsids,Bcr=[],[],[],[],[],[]
Ms,Bcr1,Bcr1Bc,S1=[],[],[],[]
names=[]
locations=''
for rec in hyst_data:
if 'er_location_name' in rec.keys() and rec['er_location_name'] not in locations: locations=locations+rec['er_location_name']+'_'
if rec['hysteresis_bcr'] !="" and rec['hysteresis_mr_moment']!="":
S.append(float(rec['hysteresis_mr_moment'])/float(rec['hysteresis_ms_moment']))
Bcr.append(float(rec['hysteresis_bcr']))
Bc.append(float(rec['hysteresis_bc']))
BcrBc.append(Bcr[-1]/Bc[-1])
if 'er_synthetic_name' in rec.keys() and rec['er_synthetic_name']!="":
rec['er_specimen_name']=rec['er_synthetic_name']
hsids.append(rec['er_specimen_name'])
names.append(rec['er_specimen_name'])
if len(rem_data)>0:
for rec in rem_data:
if rec['remanence_bcr'] !="" and float(rec['remanence_bcr'])>0:
try:
ind=hsids.index(rec['er_specimen_name'])
Bcr1.append(float(rec['remanence_bcr']))
Bcr1Bc.append(Bcr1[-1]/Bc[ind])
S1.append(S[ind])
Bcr2.append(Bcr[ind])
except ValueError:
if verbose:print('hysteresis data for ',rec['er_specimen_name'],' not found')
#
# now plot the day and S-Bc, S-Bcr plots
#
leglist=[]
if label==0:names=[]
if len(Bcr1)>0:
pmagplotlib.plotDay(DSC['day'],Bcr1Bc,S1,'ro',names=names)
pmagplotlib.plotSBcr(DSC['S-Bcr'],Bcr1,S1,'ro')
pmagplotlib.plot_init(DSC['bcr1-bcr2'],5,5)
pmagplotlib.plotBcr(DSC['bcr1-bcr2'],Bcr1,Bcr2)
else:
del DSC['bcr1-bcr2']
pmagplotlib.plotDay(DSC['day'],BcrBc,S,'bs',names=names)
pmagplotlib.plotSBcr(DSC['S-Bcr'],Bcr,S,'bs')
pmagplotlib.plotSBc(DSC['S-Bc'],Bc,S,'bs')
files={}
if len(locations)>0:locations=locations[:-1]
for key in DSC.keys():
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_'+locations+'_'+'SI:__SA:__SP:__TY:_'+key+'_.'+fmt
else: # use more readable plot naming convention
files[key] = '{}_{}.{}'.format(locations, key, fmt)
if verbose:
pmagplotlib.drawFIGS(DSC)
ans=raw_input(" S[a]ve to save plots, return to quit: ")
if ans=="a":
pmagplotlib.saveP(DSC,files)
else: sys.exit()
if plots: pmagplotlib.saveP(DSC,files)
def main():
"""
NAME
lnp_magic.py
DESCRIPTION
makes equal area projections site by site
from 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 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 'specimens.txt', ('pmag_specimens.txt' for legacy data model 2)
-fsa FILE: specify samples file, required to plot by site for data model 3 (otherwise will plot by sample)
default is 'samples.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
-sav save plots and quit
-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 criteria table # NOT IMPLEMENTED
-DM NUMBER MagIC data model (2 or 3, default 3)
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
data_model = int(float(pmag.get_named_arg("-DM", 3)))
fmt = pmag.get_named_arg("-fmt", 'svg')
if data_model == 2:
in_file = pmag.get_named_arg('-f', 'pmag_specimens.txt')
crit_file = "pmag_criteria.txt"
else:
in_file = pmag.get_named_arg('-f', 'specimens.txt')
samp_file = pmag.get_named_arg('-fsa', 'samples.txt')
crit_file = "criteria.txt"
in_file = pmag.resolve_file_name(in_file, dir_path)
dir_path = os.path.split(in_file)[0]
if data_model == 3:
samp_file = pmag.resolve_file_name(samp_file, dir_path)
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"
else:
coord = "-1"
out_file = pmag.get_named_arg('-F', '')
if out_file:
out = open(dir_path+'/'+out_file, 'w')
if '-P' in sys.argv:
make_plots = 0 # do not plot
else:
make_plots = 1 # do plot
if '-sav' in sys.argv:
plot = 1 # save plots and quit
else:
plot = 0 # show plots intereactively (if make_plots)
#
if data_model == 2:
Specs, file_type = pmag.magic_read(in_file)
if 'specimens' not in file_type:
print('Error opening ', in_file, file_type)
sys.exit()
else:
fnames = {'specimens': in_file, 'samples': samp_file}
con = cb.Contribution(dir_path, read_tables=['samples', 'specimens'],
custom_filenames=fnames)
con.propagate_name_down('site', 'specimens')
if 'site' in con.tables['specimens'].df.columns:
site_col = 'site'
else:
site_col = 'sample'
tilt_corr_col = "dir_tilt_correction"
mad_col = "dir_mad_free"
alpha95_col = "dir_alpha95"
site_alpha95_col = "dir_alpha95"
dec_col = "dir_dec"
inc_col = "dir_inc"
num_meas_col = "dir_n_measurements"
k_col = "dir_k"
cols = [site_col, tilt_corr_col, mad_col, alpha95_col, dec_col, inc_col]
con.tables['specimens'].front_and_backfill(cols)
con.tables['specimens'].df = con.tables['specimens'].df.where(con.tables['specimens'].df.notnull(), "")
Specs = con.tables['specimens'].convert_to_pmag_data_list()
## using criteria file was never fully implemented
#if '-exc' in sys.argv:
# Crits, file_type = pmag.magic_read(pmag.resolve_file_name(crit_file, dir_path))
# for crit in Crits:
# if mad_col in crit:
# M = float(crit['specimen_mad'])
# if num_meas_col in crit:
# N = float(crit['specimen_n'])
# if site_alpha95_col in crit and 'site' in crit:
# acutoff = float(crit['site_alpha95'])
# if k_col in crit:
# kcutoff = float(crit['site_k'])
#else:
# Crits = ""
sitelist = []
# initialize some variables
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
M, N, acutoff, kcutoff = 180., 1, 180., 0.
if data_model == 2:
site_col = 'er_site_name'
tilt_corr_col = "specimen_tilt_correction"
mad_col = "specimen_mad"
alpha95_col = 'specimen_alpha95'
dec_col = "specimen_dec"
inc_col = "specimen_inc"
num_meas_col = "specimen_n"
site_alpha95_col = "site_alpha95"
else: # data model 3
pass
for rec in Specs:
if rec[site_col] not in sitelist:
sitelist.append(rec[site_col])
sitelist.sort()
if make_plots == 1:
EQ = {}
EQ['eqarea'] = 1
for site in sitelist:
pmagplotlib.plot_init(EQ['eqarea'], 4, 4)
print(site)
data = []
for spec in Specs:
if tilt_corr_col not in list(spec.keys()):
spec[tilt_corr_col] = '-1' # assume unoriented
if spec[site_col] == site:
if mad_col not in list(spec.keys()) or spec[mad_col] == "":
if alpha95_col in list(spec.keys()) and spec[alpha95_col] != "":
spec[mad_col] = spec[alpha95_col]
else:
spec[mad_col] = '180'
if not spec[num_meas_col]:
continue
if (float(spec[tilt_corr_col]) == float(coord)) and (float(spec[mad_col]) <= M) and (float(spec[num_meas_col]) >= N):
rec = {}
for key in list(spec.keys()):
rec[key] = spec[key]
rec["dec"] = float(spec[dec_col])
rec["inc"] = float(spec[inc_col])
rec["tilt_correction"] = spec[tilt_corr_col]
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 make_plots == 1:
files = {}
files['eqarea'] = site+'_'+crd+'_'+'eqarea'+'.'+fmt
pmagplotlib.plot_lnp(EQ['eqarea'], site,
data, fpars, 'specimen_direction_type')
if plot == 0:
pmagplotlib.draw_figs(EQ)
ans = input(
"s[a]ve plot, [q]uit, <return> to continue:\n ")
if ans == "a":
pmagplotlib.save_plots(EQ, files)
if ans == "q":
sys.exit()
else:
pmagplotlib.save_plots(EQ, files)
else:
print('skipping site - not enough data with specified coordinate system')
def main():
"""
NAME
basemap_magic.py
NB: this program no longer maintained - use plot_mapPTS.py for greater functionality
DESCRIPTION
makes a map of locations in er_sites.txt
SYNTAX
basemap_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f SFILE, specify er_sites.txt or pmag_results.txt format file
-res [c,l,i,h] specify resolution (crude,low,intermediate,high)
-etp plot the etopo20 topographic mesh
-pad [LAT LON] pad bounding box by LAT/LON (default is [.5 .5] degrees)
-grd SPACE specify grid spacing
-prj [lcc] , specify projection (lcc=lambert conic conformable), default is mercator
-n print site names (default is not)
-l print location names (default is not)
-o color ocean blue/land green (default is not)
-R don't plot details of rivers
-B don't plot national/state boundaries, etc.
-sav save plot and quit quietly
-fmt [png,svg,eps,jpg,pdf] specify format for output, default is pdf
DEFAULTS
SFILE: 'er_sites.txt'
resolution: intermediate
saved images are in pdf
"""
dir_path='.'
sites_file='er_sites.txt'
ocean=0
res='i'
proj='merc'
prn_name=0
prn_loc=0
fancy=0
rivers,boundaries=0,0
padlon,padlat,gridspace,details=.5,.5,.5,1
fmt='pdf'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sites_file=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if '-etp' in sys.argv:fancy=1
if '-n' in sys.argv:prn_name=1
if '-l' in sys.argv:prn_loc=1
if '-o' in sys.argv:ocean=1
if '-R' in sys.argv:rivers=0
if '-B' in sys.argv:boundaries=0
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
verbose=pmagplotlib.verbose
if '-sav' in sys.argv:
verbose=0
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
sites_file=dir_path+'/'+sites_file
location=""
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
# read in er_sites file
Sites,file_type=pmag.magic_read(sites_file)
if 'results' in file_type:
latkey='average_lat'
lonkey='average_lon'
namekey='pmag_result_name'
lockey='er_location_names'
else:
latkey='site_lat'
lonkey='site_lon'
namekey='er_site_name'
lockey='er_location_name'
lats,lons=[],[]
slats,slons=[],[]
names,locs=[],[]
for site in Sites:
if prn_loc==1 and location=="":location=site['er_location_name']
lats.append(float(site[latkey]))
l=float(site[lonkey])
if l<0:l=l+360. # make positive
lons.append(l)
if prn_name==1:names.append(site[namekey])
if prn_loc==1:locs.append(site[lockey])
for lat in lats:slats.append(lat)
for lon in lons:slons.append(lon)
Opts={'res':res,'proj':proj,'loc_name':locs,'padlon':padlon,'padlat':padlat,'latmin':numpy.min(slats)-padlat,'latmax':numpy.max(slats)+padlat,'lonmin':numpy.min(slons)-padlon,'lonmax':numpy.max(slons)+padlon,'sym':'ro','boundinglat':0.,'pltgrid':1.}
Opts['lon_0']=0.5*(numpy.min(slons)+numpy.max(slons))
Opts['lat_0']=0.5*(numpy.min(slats)+numpy.max(slats))
Opts['names']=names
Opts['gridspace']=gridspace
Opts['details']={'coasts':1,'rivers':1,'states':1,'countries':1,'ocean':0}
if ocean==1:Opts['details']['ocean']=1
if rivers==1: Opts['details']['rivers']=0
if boundaries==1:
Opts['details']['states']=0
Opts['details']['countries']=0
Opts['details']['fancy']=fancy
pmagplotlib.plotMAP(FIG['map'],lats,lons,Opts)
if verbose:pmagplotlib.drawFIGS(FIG)
files={}
for key in FIG.keys():
files[key]='Site_map'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['map']='Site Map'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
elif verbose:
ans=raw_input(" S[a]ve to save plot, Return to quit: ")
if ans=="a":
pmagplotlib.saveP(FIG,files)
else:
pmagplotlib.saveP(FIG,files)
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: magic_measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols (for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['demag']=1 # demag is figure 1
in_file,plot_key,LT='magic_measurements.txt','er_location_name',"LT-AF-Z"
XLP=""
norm=1
LT='LT-AF-Z'
units,dmag_key='T','treatment_ac_field'
plot=0
fmt='svg'
if len(sys.argv)>1:
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-N' in sys.argv: norm=0
if '-sav' in sys.argv:
plot=1
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
if '-XLP' in sys.argv:
ind=sys.argv.index("-XLP")
XLP=sys.argv[ind+1] # get lab protocol for excluding
if '-LT' in sys.argv:
ind=sys.argv.index("-LT")
LT='LT-'+sys.argv[ind+1]+'-Z' # get lab treatment for plotting
if LT=='LT-T-Z':
units,dmag_key='K','treatment_temp'
elif LT=='LT-AF-Z':
units,dmag_key='T','treatment_ac_field'
elif LT=='LT-M-Z':
units,dmag_key='J','treatment_mw_energy'
else:
units='U'
data,file_type=pmag.magic_read(in_file)
sids=pmag.get_specs(data)
pmagplotlib.plot_init(FIG['demag'],5,5)
print len(data),' records read from ',in_file
#
#
# find desired intensity data
#
#
plotlist,intlist=[],['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
IntMeths=[]
FixData=[]
for rec in data:
meths=[]
methcodes=rec['magic_method_codes'].split(':')
for meth in methcodes:meths.append(meth.strip())
for key in rec.keys():
if key in intlist and rec[key]!="":
if key not in IntMeths:IntMeths.append(key)
if rec[plot_key] not in plotlist and LT in meths: plotlist.append(rec[plot_key])
if 'measurement_flag' not in rec.keys():rec['measurement_flag']='g'
FixData.append(rec)
plotlist.sort()
if len(IntMeths)==0:
print 'No intensity information found'
sys.exit()
data=FixData
int_key=IntMeths[0] # plot first intensity method found - normalized to initial value anyway - doesn't matter which used
for plt in plotlist:
if plot==0: print plt,'plotting by: ',plot_key
PLTblock=pmag.get_dictitem(data,plot_key,plt,'T') # fish out all the data for this type of plot
PLTblock=pmag.get_dictitem(PLTblock,'magic_method_codes',LT,'has') # fish out all the dmag for this experiment type
PLTblock=pmag.get_dictitem(PLTblock,int_key,'','F') # get all with this intensity key non-blank
if XLP!="":PLTblock=pmag.get_dictitem(PLTblock,'magic_method_codes',XLP,'not') # reject data with XLP in method_code
if len(PLTblock)>2:
title=PLTblock[0][plot_key]
spcs=[]
for rec in PLTblock:
if rec['er_specimen_name'] not in spcs:spcs.append(rec['er_specimen_name'])
for spc in spcs:
SPCblock=pmag.get_dictitem(PLTblock,'er_specimen_name',spc,'T') # plot specimen by specimen
INTblock=[]
for rec in SPCblock:
INTblock.append([float(rec[dmag_key]),0,0,float(rec[int_key]),1,rec['measurement_flag']])
if len(INTblock)>2:
pmagplotlib.plotMT(FIG['demag'],INTblock,title,0,units,norm)
if plot==1:
files={}
for key in FIG.keys():
files[key]=title+'_'+LT+'.'+fmt
pmagplotlib.saveP(FIG,files)
sys.exit()
else:
pmagplotlib.drawFIGS(FIG)
ans=raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=='q':sys.exit()
if ans=="a":
files={}
for key in FIG.keys():
files[key]=title+'_'+LT+'.svg'
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['demag'])
def main():
"""
NAME
customize_criteria.py
NB: This program has been deprecated - use demag_gui or thellier_gui
to customize acceptance criteria - OR pandas from within a jupyter notebook
DESCRIPTION
Allows user to specify acceptance criteria, saves them in pmag_criteria.txt
SYNTAX
customize_criteria.py [-h][command line options]
OPTIONS
-h prints help message and quits
-f IFILE, reads in existing criteria
-F OFILE, writes to pmag_criteria format file
DEFAULTS
IFILE: pmag_criteria.txt
OFILE: pmag_criteria.txt
OUTPUT
creates a pmag_criteria.txt formatted output file
"""
infile, critout = "", "pmag_criteria.txt"
# parse command line options
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
infile = sys.argv[ind + 1]
crit_data, file_type = pmag.magic_read(infile)
if file_type != 'pmag_criteria':
print('bad input file')
print(main.__doc__)
sys.exit()
print("Acceptance criteria read in from ", infile)
if '-F' in sys.argv:
ind = sys.argv.index('-F')
critout = sys.argv[ind + 1]
Dcrit, Icrit, nocrit = 0, 0, 0
custom = '1'
crit = input(
" [0] Use no acceptance criteria?\n [1] Use default criteria\n [2] customize criteria \n "
)
if crit == '0':
print('Very very loose criteria saved in ', critout)
crit_data = pmag.default_criteria(1)
pmag.magic_write(critout, crit_data, 'pmag_criteria')
sys.exit()
crit_data = pmag.default_criteria(0)
if crit == '1':
print('Default criteria saved in ', critout)
pmag.magic_write(critout, crit_data, 'pmag_criteria')
sys.exit()
CritRec = crit_data[0]
crit_keys = list(CritRec.keys())
crit_keys.sort()
print(
"Enter new threshold value.\n Return to keep default.\n Leave blank to not use as a criterion\n "
)
for key in crit_keys:
if key != 'pmag_criteria_code' and key != 'er_citation_names' and key != 'criteria_definition' and CritRec[
key] != "":
print(key, CritRec[key])
new = input('new value: ')
if new != "": CritRec[key] = (new)
pmag.magic_write(critout, [CritRec], 'pmag_criteria')
print("Criteria saved in pmag_criteria.txt")
def main():
"""
NAME
plotxy_magic.py
DESCRIPTION
Makes simple X,Y plots
INPUT FORMAT
Any MagIC formatted file
SYNTAX
plotxy_magic.py [command line options]
OPTIONS
-h prints this help message
-f FILE to set file name on command rec
-c col1 col2 specify columns names to plot
-sym SYM SIZE specify symbol and size to plot: default is red dots
-S don't plot symbols
-xlab XLAB
-ylab YLAB
-l connect symbols with lines
-b xmin xmax ymin ymax, sets bounds
# -b [key:max:min,key:max:min,etc.] leave or min blank for no cutoff
"""
col1,col2=0,1
sym,size = 'ro',20
xlab,ylab='',''
lines=0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
else:
'-f option is a required field'
print(main.__doc__)
sys.exit()
if '-c' in sys.argv:
ind=sys.argv.index('-c')
col1=sys.argv[ind+1]
col2=sys.argv[ind+2]
else:
'Column headers a required field'
print(main.__doc__)
sys.exit()
if '-xlab' in sys.argv:
ind=sys.argv.index('-xlab')
xlab=sys.argv[ind+1]
if '-ylab' in sys.argv:
ind=sys.argv.index('-ylab')
ylab=sys.argv[ind+1]
# if '-b' in sys.argv:
# ind=sys.argv.index('-b')
# bounds=sys.argv[ind+1].split(',')
if '-b' in sys.argv:
ind=sys.argv.index('-b')
xmin=float(sys.argv[ind+1])
xmax=float(sys.argv[ind+2])
ymin=float(sys.argv[ind+3])
ymax=float(sys.argv[ind+4])
if '-sym' in sys.argv:
ind=sys.argv.index('-sym')
sym=sys.argv[ind+1]
size=int(sys.argv[ind+2])
if '-l' in sys.argv: lines=1
if '-S' in sys.argv: sym=''
X,Y=[],[]
data,file_type=pmag.magic_read(file)
print(file_type)
for rec in data:
if col1 not in list(rec.keys()) or col2 not in list(rec.keys()):
print(col1,' and/or ',col2, ' not in file headers')
print('try again')
sys.exit()
if rec[col1]!='' and rec[col2]!='':
skip=0
if '-crit' in sys.argv:
for crit in bounds:
crits=crit.split(':')
crit_key=crits[0]
crit_min=crits[1]
crit_max=crits[2]
if rec[crit_key]=="":
skip=1
else:
if crit_min!="" and float(rec[crit_key])<float(crit_min):skip=1
if crit_max!="" and float(rec[crit_key])>float(crit_min):skip=1
if skip==0:
X.append(float(rec[col1]))
Y.append(float(rec[col2]))
if len(X)==0:
print(col1,' and/or ',col2, ' have no data ')
print('try again')
sys.exit()
else:
print(len(X),' data points')
if sym!='':pylab.scatter(X,Y,c=sym[0],marker=sym[1],s=size)
if xlab!='':pylab.xlabel(xlab)
if ylab!='':pylab.ylabel(ylab)
if lines==1:pylab.plot(X,Y,'k-')
if '-b' in sys.argv:pylab.axis([xmin,xmax,ymin,ymax])
pylab.draw()
ans=input("Press return to quit ")
sys.exit()
def main(command_line=True, **kwargs):
"""
NAME
iodp_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
iodp_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'r')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'r')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave = 0
volume = 2.5**3 #default volume is a 2.5cm cube
inst = ""
samp_con, Z = '5', ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = 'This study'
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
dir_path = '.'
MagRecs = []
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print(main.__doc__)
return False
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-fsa' in args:
ind = args.index("-fsa")
samp_file = args[ind + 1]
if samp_file[0] != '/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file, 'r')
ErSamps, file_type = pmag.magic_read(samp_file)
except:
print(samp_file, ' not found: ')
print(
' download csv file and import to MagIC with iodp_samples_magic.py'
)
if '-f' in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args:
noave = 1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print("You must provide an IODP_jr6 format file")
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print(
'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'
.format(mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(
mag_file)
if not os.path.exists(samp_file):
print(
"Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one"
.format(input_dir_path))
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(
input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
samples, filetype = pmag.magic_read(samp_file)
with open(temp, 'r') as finput:
lines = finput.readlines()
os.remove(temp)
for line in lines:
MagRec = {}
line = line.split()
spec_text_id = line[0].split('_')[1]
SampRecs = pmag.get_dictitem(samples, 'er_sample_alternatives',
spec_text_id, 'has')
if len(SampRecs) > 0: # found one
MagRec['er_specimen_name'] = SampRecs[0]['er_sample_name']
MagRec['er_sample_name'] = MagRec['er_specimen_name']
MagRec['er_site_name'] = MagRec['er_specimen_name']
MagRec["er_citation_names"] = "This study"
MagRec['er_location_name'] = er_location_name
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["treatment_ac_field"] = '0'
volume = float(SampRecs[0]['sample_volume'])
x = float(line[4])
y = float(line[3])
negz = float(line[2])
cart = np.array([x, y, -negz]).transpose()
direction = pmag.cart2dir(cart).transpose()
expon = float(line[5])
magn_volume = direction[2] * (10.0**expon)
moment = magn_volume * volume
MagRec["measurement_magn_moment"] = str(moment)
MagRec["measurement_magn_volume"] = str(
magn_volume) #str(direction[2] * (10.0 ** expon))
MagRec["measurement_dec"] = '%7.1f' % (direction[0])
MagRec["measurement_inc"] = '%7.1f' % (direction[1])
step = line[1]
if step == 'NRM':
meas_type = "LT-NO"
elif step[0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(step[2:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif step[0:2] == 'TD':
meas_type = "LT-T-Z"
treat = float(step[2:])
MagRec["treatment_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
elif step[0:3] == 'ARM': #
meas_type = "LT-AF-I"
treat = float(row['step'][3:])
MagRec["treatment_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"] = '%8.3e' % (
50e-6) # assume 50uT DC field
MagRec[
"measurement_description"] = 'Assumed DC field - actual unknown'
elif step[0:3] == 'IRM': #
meas_type = "LT-IRM"
treat = float(step[3:])
MagRec["treatment_dc_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
else:
print('unknown treatment type for ', row)
return False, 'unknown treatment type for ', row
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec.copy())
else:
print('sample name not found: ', row['specname'])
MagOuts = pmag.measurements_methods(MagRecs, noave)
file_created, error_message = pmag.magic_write(meas_file, MagOuts,
'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main(command_line=True, **kwargs):
"""
NAME
_2g_bin_magic.py
DESCRIPTION
takes the binary 2g format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2g_bin_magic.py [command line options]
OPTIONS
-f FILE: specify input 2g (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sites.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
mag_file = ''
specnum=0
ub_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","3","1","magic_measurements.txt"
pos_file,site_file="","er_sites.txt"
noave=1
args=sys.argv
bed_dip,bed_dip_dir="",""
samp_con,Z,average_bedding="2",1,"0"
meths='FS-FD'
sclass,lithology,_type="","",""
user,inst="",""
DecCorr=0.
location_name="unknown"
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
gmeths=""
#
#
dir_path='.'
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in args:
print main.__doc__
return False
if "-f" in args:
ind=args.index("-f")
mag_file=sys.argv[ind+1]
if "-fpos" in args:
ind=args.index("-fpos")
pos_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
meas_file=sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-Fsi" in args:
ind=args.index("-Fsi")
site_file=sys.argv[ind+1]
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-mcd" in args:
ind=args.index("-mcd")
gmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-a" in args:
noave=0
#
ID = False
if '-ID' in args:
ind = args.index('-ID')
ID = args[ind+1]
#
if not command_line:
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
pos_file = kwargs.get('pos_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', '')
location_name = kwargs.get('location_name', '')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 1) # default is DO average
ID = kwargs.get('ID', '')
# format and fix variables acquired from command line args or input with **kwargs
if specnum!=0:specnum=-specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "6" in samp_con:
try:
Samps,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
except:
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if file_type == 'bad_file':
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if not mag_file:
print "mag file is required input"
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = output_dir_path+'/'+samp_file
site_file = output_dir_path+'/'+site_file
meas_file= output_dir_path+'/'+meas_file
samplist=[]
try:
Samps,file_type=pmag.magic_read(samp_file)
for samp in Samps:
if samp['er_sample_name'] not in samplist: samplist.append(samp['er_sample_name'])
except:
Samps=[]
MagRecs=[]
try:
f=open(mag_file,'rU')
input=f.read()
f.close()
except Exception as ex:
print 'ex', ex
print "bad mag file"
return False, "bad mag file"
firstline,date=1,""
d=input.split('\xcd')
for line in d:
rec=line.split('\x00')
if firstline==1:
firstline=0
spec,vol="",1
for c in line[15:23]:
if c!='\x00':spec=spec+c
# check for bad sample name
test=spec.split('.')
date=""
if len(test)>1:
spec=test[0]
kk=24
while line[kk]!='\x01' and line[kk]!='\x00':
kk+=1
vcc=line[24:kk]
el=10
while rec[el].strip()!='':el+=1
date,comments=rec[el+7],[]
else:
el=9
while rec[el]!='\x01':el+=1
vcc,date,comments=rec[el-3],rec[el+7],[]
specname=spec.lower()
print 'importing ',specname
el+=8
while rec[el].isdigit()==False:
comments.append(rec[el])
el+=1
while rec[el]=="":el+=1
az=float(rec[el])
el+=1
while rec[el]=="":el+=1
pl=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip_dir=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip=float(rec[el])
el+=1
while rec[el]=="":el+=1
if rec[el]=='\x01':
bed_dip=180.-bed_dip
el+=1
while rec[el]=="":el+=1
fold_az=float(rec[el])
el+=1
while rec[el]=="":el+=1
fold_pl=rec[el]
el+=1
while rec[el]=="":el+=1
if rec[el]!="" and rec[el]!='\x02' and rec[el]!='\x01':
deccorr=float(rec[el])
az+=deccorr
bed_dip_dir+=deccorr
fold_az+=deccorr
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
if az>=360.:az=az-360.
if fold_az>=360.:fold_az=fold_az-360.
else:
deccorr=0
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
SampRec={}
SampRec["er_sample_name"]=sample
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"]='%7.1f'%(bed_dip)
SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
if vcc.strip()!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SampRec["sample_volume"]='%10.3e'%(vol) #
SampRec["sample_class"]=sclass
SampRec["sample_lithology"]=lithology
SampRec["sample_type"]=_type
SampRec["sample_declination_correction"]='%7.1f'%(deccorr)
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths=""
for meth in methods:meths=meths+meth+":"
meths=meths[:-1]
SampRec["magic_method_codes"]=meths
if int(samp_con)<6 or int(samp_con) == 7:
site=pmag.parse_site(SampRec["er_sample_name"],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
elif len(Samps)>1:
site,location="",""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site=samp["er_site_name"]
location=samp["er_location_name"]
break
SampRec["er_location_name"]=samp["er_location_name"]
SampRec["er_site_name"]=samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
MagRec={}
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=specname
MagRec["er_sample_name"]=SampRec['er_sample_name']
MagRec["er_site_name"]=SampRec['er_site_name']
MagRec["er_location_name"]=location_name
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MagRec["measurement_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MagRec["measurement_inc"]=rec[el]
cinc=float(rec[el])
el+=1
while rec[el]=="":el+=1
gdec=rec[el]
el+=1
while rec[el]=="":el+=1
ginc=rec[el]
el=skip(2,el,rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MagRec["measurement_sd_x"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MagRec["measurement_sd_y"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MagRec["measurement_sd_z"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MagRec["measurement_positions"]=rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (float(treat[:-1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
MagOuts, keylist = pmag.fillkeys(MagOuts)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "Measurements put in ",meas_file
SampsOut,sampkeys=pmag.fillkeys(Samps)
pmag.magic_write(samp_file,SampsOut,"er_samples")
Sites=[]
for samp in Samps:
SiteRec={}
SiteRec['er_site_name']=samp['er_site_name']
SiteRec['er_location_name']=samp['er_location_name']
SiteRec['site_definition']='s'
SiteRec['er_citation_names']='This study'
if 'sample_class' in samp.keys():SiteRec['site_class']=samp['sample_class']
if 'sample_lithology' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_type' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_lat' in samp.keys():
SiteRec['site_lat']=samp['sample_lat']
else:
SiteRec['site_lat']="-999"
if 'sample_lon' in samp.keys():
SiteRec['site_lon']=samp['sample_lon']
else:
SiteRec['site_lon']="-999"
if 'sample_height' in samp.keys():SiteRec['site_height']=samp['sample_height']
Sites.append(SiteRec)
pmag.magic_write(site_file,Sites,'er_sites')
return True, meas_file
def main():
"""
NAME
sites_locations.py
DESCRIPTION
reads in er_sites.txt file and finds all locations and bounds of locations
outputs er_locations.txt file
SYNTAX
sites_locations.py [command line options]
OPTIONS
-h prints help message and quits
-f: specimen input er_sites format file, default is "er_sites.txt"
-F: locations table: default is "er_locations.txt"
"""
# set defaults
site_file = "er_sites.txt"
loc_file = "er_locations.txt"
Names, user = [], "unknown"
Done = []
version_num = pmag.get_version()
args = sys.argv
dir_path = '.'
# get command line stuff
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if '-f' in args:
ind = args.index("-f")
site_file = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
loc_file = args[ind + 1]
#
site_file = dir_path + '/' + site_file
loc_file = dir_path + '/' + loc_file
Sites, file_type = pmag.magic_read(site_file)
if file_type != 'er_sites':
print(file_type)
print(file_type, "This is not a valid er_sites file ")
sys.exit()
# read in site data
#
LocNames, Locations = [], []
for site in Sites:
if site['er_location_name'] not in LocNames: # new location name
LocNames.append(site['er_location_name'])
sites_locs = pmag.get_dictitem(Sites, 'er_location_name',
site['er_location_name'],
'T') # get all sites for this loc
lats = pmag.get_dictkey(sites_locs, 'site_lat',
'f') # get all the latitudes as floats
lons = pmag.get_dictkey(sites_locs, 'site_lon',
'f') # get all the longitudes as floats
LocRec = {
'er_citation_names': 'This study',
'er_location_name': site['er_location_name'],
'location_type': ''
}
LocRec['location_begin_lat'] = str(min(lats))
LocRec['location_end_lat'] = str(max(lats))
LocRec['location_begin_lon'] = str(min(lons))
LocRec['location_end_lon'] = str(max(lons))
Locations.append(LocRec)
if len(Locations) > 0:
pmag.magic_write(loc_file, Locations, "er_locations")
print("Locations written to: ", loc_file)
def main():
"""
NAME
chi_magic.py
DESCRIPTION
plots magnetic susceptibility as a function of frequency and temperature and AC field
SYNTAX
chi_magic.py [command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of FILE and temperature step
-f FILE, specify magic_measurements format file
-T IND, specify temperature step to plot
-e EXP, specify experiment name to plot
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-sav save figure and quit
DEFAULTS
FILE: magic_measurements.txt
IND: first
SPEC: step through one by one
"""
cont,FTinit,BTinit,k="",0,0,0
meas_file="magic_measurements.txt"
spec=""
Tind,cont=0,""
EXP=""
fmt='svg' # default image type for saving
plot=0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-i' in sys.argv:
file=input("Input magic_measurements file name? [magic_measurements.txt] ")
if file!="":meas_file=file
if '-e' in sys.argv:
ind=sys.argv.index('-e')
EXP=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-T' in sys.argv:
ind=sys.argv.index('-T')
Tind=int(sys.argv[ind+1])
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
#
meas_data,file_type=pmag.magic_read(meas_file)
#
# get list of unique experiment names
#
# initialize some variables (a continuation flag, plot initialization flags and the experiment counter
experiment_names=[]
for rec in meas_data:
if rec['magic_experiment_name'] not in experiment_names:experiment_names.append(rec['magic_experiment_name'])
#
# hunt through by experiment name
if EXP!="":
try:
k=experiment_names.index(EXP)
except:
print("Bad experiment name")
sys.exit()
while k < len(experiment_names):
e=experiment_names[k]
if EXP=="":print(e, k+1 , 'out of ',len(experiment_names))
#
# initialize lists of data, susceptibility, temperature, frequency and field
X,T,F,B=[],[],[],[]
for rec in meas_data:
methcodes=rec['magic_method_codes']
meths=methcodes.strip().split(':')
if rec['magic_experiment_name']==e and "LP-X" in meths: # looking for chi measurement
if 'measurement_temp' not in list(rec.keys()):rec['measurement_temp']='300' # set defaults
if 'measurement_freq' not in list(rec.keys()):rec['measurement_freq']='0' # set defaults
if 'measurement_lab_field_ac' not in list(rec.keys()):rec['measurement_lab_field_ac']='0' # set default
X.append(float(rec['measurement_x']))
T.append(float(rec['measurement_temp']))
F.append(float(rec['measurement_freq']))
B.append(float(rec['measurement_lab_field_ac']))
#
# get unique list of Ts,Fs, and Bs
#
Ts,Fs,Bs=[],[],[]
for k in range(len(X)): # hunt through all the measurements
if T[k] not in Ts:Ts.append(T[k]) # append if not in list
if F[k] not in Fs:Fs.append(F[k])
if B[k] not in Bs:Bs.append(B[k])
Ts.sort() # sort list of temperatures, frequencies and fields
Fs.sort()
Bs.sort()
if '-x' in sys.argv:
k=len(experiment_names)+1 # just plot the one
else:
k+=1 # increment experiment number
#
# plot chi versus T and F holding B constant
#
plotnum=1 # initialize plot number to 1
if len(X)>2: # if there are any data to plot, continue
b=Bs[-1] # keeping field constant and at maximum
XTF=[] # initialize list of chi versus Temp and freq
for f in Fs: # step through frequencies sequentially
XT=[] # initialize list of chi versus temp
for kk in range(len(X)): # hunt through all the data
if F[kk]==f and B[kk]==b: # select data with given freq and field
XT.append([X[kk],T[kk]]) # append to list
XTF.append(XT) # append list to list of frequencies
if len(XT)>1: # if there are any temperature dependent data
pmagplotlib.plot_init(plotnum,5,5) # initialize plot
pmagplotlib.plotXTF(plotnum,XTF,Fs,e,b) # call the plotting function
if plot==0:pmagplotlib.drawFIGS({'fig':plotnum}) #make it visible
plotnum+=1 # increment plot number
f=Fs[0] # set frequency to minimum
XTB=[] # initialize list if chi versus Temp and field
for b in Bs: # step through field values
XT=[] # initial chi versus temp list for this field
for kk in range(len(X)): # hunt through all the data
if F[kk]==f and B[kk]==b: # select data with given freq and field
XT.append([X[kk],T[kk]]) # append to list
XTB.append(XT)
if len(XT)>1: # if there are any temperature dependent data
pmagplotlib.plot_init(plotnum,5,5) # set up plot
pmagplotlib.plotXTB(plotnum,XTB,Bs,e,f) # call the plotting function
if plot==0:pmagplotlib.drawFIGS({'fig':plotnum})
plotnum+=1 # increment plot number
if '-i' in sys.argv:
for ind in range(len(Ts)): # print list of temperatures available
print(ind,int(Ts[ind]))
cont=input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=='a':
files={}
PLTS={}
for p in range(1,plotnum):
key=str(p)
files[key]=e+'_'+key+'.'+fmt
PLTS[key]=key
pmagplotlib.saveP(PLTS,files)
cont=input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=="":cont='q'
while cont!="q":
if '-i' in sys.argv:Tind=int(cont) # set temperature index
b=Bs[-1] # set field to max available
XF=[] # initial chi versus frequency list
for kk in range(len(X)): # hunt through the data
if T[kk]==Ts[Tind] and B[kk]==b: # if temperature and field match,
XF.append([X[kk],F[kk]]) # append the data
if len(XF)>1: # if there are any data to plot
if FTinit==0: # if not already initialized, initialize plot
#print 'initializing ',plotnum
pmagplotlib.plot_init(plotnum,5,5)
FTinit=1
XFplot=plotnum
plotnum+=1 # increment plotnum
pmagplotlib.plotXFT(XFplot,XF,Ts[Tind],e,b)
if plot==0:pmagplotlib.drawFIGS({'fig':plotnum})
else:
print('\n *** Skipping susceptibitily-frequency plot as a function of temperature *** \n')
f=Fs[0] # set frequency to minimum available
XB=[] # initialize chi versus field list
for kk in range(len(X)): # hunt through the data
if T[kk]==Ts[Tind] and F[kk]==f: # if temperature and field match those desired
XB.append([X[kk],B[kk]]) # append the data to list
if len(XB)>4: # if there are any data
if BTinit==0: # if plot not already initialized
pmagplotlib.plot_init(plotnum,5,5) # do it
BTinit=1
pmagplotlib.plotXBT(plotnum,XB,Ts[Tind],e,f) # and call plotting function
if plot==0:pmagplotlib.drawFIGS({'fig':plotnum})
else:
print('Skipping susceptibitily - AC field plot as a function of temperature')
files={}
PLTS={}
for p in range(1,plotnum):
key=str(p)
files[key]=e+'_'+key+'.'+fmt
PLTS[key]=p
if '-i' in sys.argv:
for ind in range(len(Ts)): # just in case you forgot, print out a new list of temperatures
print(ind,int(Ts[ind]))
cont=input("Enter index of next temperature step, s[a]ve plots, [return] to quit ") # ask for new temp
if cont=="":sys.exit()
if cont=='a':
pmagplotlib.saveP(PLTS,files)
cont=input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=="":sys.exit()
elif plot==0:
ans=input("enter s[a]ve to save files, [return] to quit ")
if ans=='a':
pmagplotlib.saveP(PLTS,files)
sys.exit()
else:
sys.exit()
else:
pmagplotlib.saveP(PLTS,files)
sys.exit()
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
"""
dirlist=['./']
dir_path=os.getcwd()
names=os.listdir(dir_path)
for n in names:
if 'Location' in n:
dirlist.append(n)
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
else: fmt='png'
if '-f' in sys.argv:
ind=sys.argv.index("-f")
filelist=[sys.argv[ind+1]]
else:
filelist=os.listdir(dir_path)
if '-h' in sys.argv:
print main.__doc__
sys.exit()
for loc in dirlist:
print 'working on: ',loc
os.chdir(loc) # change working directories to each location
crd='s'
if 'er_samples.txt' in filelist: # find coordinate systems
samps,file_type=pmag.magic_read('er_samples.txt') # read in data
Srecs=pmag.get_dictitem(samps,'sample_azimuth','','F')# get all none blank sample orientations
if len(Srecs)>0:
crd='g'
if 'magic_measurements.txt' in filelist: # start with measurement data
print 'working on measurements data'
data,file_type=pmag.magic_read('magic_measurements.txt') # read in data
if loc == './': data=pmag.get_dictitem(data,'er_location_name','','T') # get all the blank location names from data file
# looking for zeq_magic possibilities
AFZrecs=pmag.get_dictitem(data,'magic_method_codes','LT-AF-Z','has')# get all none blank method codes
TZrecs=pmag.get_dictitem(data,'magic_method_codes','LT-T-Z','has')# get all none blank method codes
MZrecs=pmag.get_dictitem(data,'magic_method_codes','LT-M-Z','has')# get all none blank method codes
Drecs=pmag.get_dictitem(data,'measurement_dec','','F') # get all dec measurements
Irecs=pmag.get_dictitem(data,'measurement_inc','','F') # get all dec measurements
Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
for key in Mkeys:
Mrecs=pmag.get_dictitem(data,key,'','F') # get intensity data
if len(Mrecs)>0:break
if len(AFZrecs)>0 or len(TZrecs)>0 or len(MZrecs)>0 and len(Drecs)>0 and len(Irecs)>0 and len(Mrecs)>0: # potential for stepwise demag curves
print 'zeq_magic.py -fsp pmag_specimens.txt -sav -fmt '+fmt+' -crd '+crd
os.system('zeq_magic.py -sav -fmt '+fmt+' -crd '+crd )
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data,'magic_method_codes','LP-PI-TRM','has'))>0:
print 'thellier_magic.py -fsp pmag_specimens.txt -sav -fmt '+fmt
os.system('thellier_magic.py -sav -fmt '+fmt)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data,'magic_method_codes','LP-HYS','has'))>0: # find hyst experiments
print 'quick_hyst.py -sav -fmt '+fmt
os.system('quick_hyst.py -sav -fmt '+fmt)
if 'pmag_results.txt' in filelist: # start with measurement data
data,file_type=pmag.magic_read('pmag_results.txt') # read in data
print 'number of datapoints: ',len(data)
if loc == './': data=pmag.get_dictitem(data,'er_location_names',':','has') # get all the concatenated location names from data file
print 'number of datapoints: ',len(data) ,loc
print 'working on pmag_results directions'
SiteDIs=pmag.get_dictitem(data,'average_dec',"",'F') # find decs
print 'number of directions: ',len(SiteDIs)
SiteDIs=pmag.get_dictitem(SiteDIs,'average_inc',"",'F') # find decs and incs
print 'number of directions: ',len(SiteDIs)
SiteDIs=pmag.get_dictitem(SiteDIs,'data_type','i','has') # only individual results - not poles
print 'number of directions: ',len(SiteDIs)
SiteDIs_t=pmag.get_dictitem(SiteDIs,'tilt_correction','100','T')# tilt corrected coordinates
print 'number of directions: ',len(SiteDIs)
if len(SiteDIs_t)>0:
print 'eqarea_magic.py -sav -crd t -fmt '+fmt
os.system('eqarea_magic.py -sav -crd t -fmt '+fmt)
elif len(SiteDIs)>0 and 'tilt_correction' not in SiteDIs[0].keys():
print 'eqarea_magic.py -sav -fmt '+fmt
os.system('eqarea_magic.py -sav -fmt '+fmt)
else:
SiteDIs_g=pmag.get_dictitem(SiteDIs,'tilt_correction','0','T')# geographic coordinates
if len(SiteDIs_g)>0:
print 'eqarea_magic.py -sav -crd g -fmt '+fmt
os.system('eqarea_magic.py -sav -crd g -fmt '+fmt)
else:
SiteDIs_s=pmag.get_dictitem(SiteDIs,'tilt_correction','-1','T')# sample coordinates
if len(SiteDIs_s)>0:
print 'eqarea_magic.py -sav -crd s -fmt '+fmt
os.system('eqarea_magic.py -sav -crd s -fmt '+fmt)
else:
SiteDIs_x=pmag.get_dictitem(SiteDIs,'tilt_correction','','T')# no coordinates
if len(SiteDIs_x)>0:
print 'eqarea_magic.py -sav -fmt '+fmt
os.system('eqarea_magic.py -sav -fmt '+fmt)
print 'working on pmag_results VGP map'
VGPs=pmag.get_dictitem(SiteDIs,'vgp_lat',"",'F') # are there any VGPs?
if len(VGPs)>0: # YES!
os.system('vgpmap_magic.py -prj moll -res c -sym ro 5 -sav -fmt png')
print 'working on pmag_results intensities'
os.system('magic_select.py -f pmag_results.txt -key data_type i T -F tmp.txt')
os.system('magic_select.py -f tmp.txt -key average_int 0. has -F tmp1.txt')
os.system("grab_magic_key.py -f tmp1.txt -key average_int | awk '{print $1*1e6}' >tmp2.txt")
data,file_type=pmag.magic_read('tmp1.txt') # read in data
locations=pmag.get_dictkey(data,'er_location_names',"")
histfile='LO:_'+locations[0]+'_intensities_histogram:_.'+fmt
os.system("histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " +histfile)
print "histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " +histfile
os.system('rm tmp*.txt')
if 'rmag_hysteresis.txt' in filelist: # start with measurement data
print 'working on rmag_hysteresis'
data,file_type=pmag.magic_read('rmag_hysteresis.txt') # read in data
if loc == './': data=pmag.get_dictitem(data,'er_location_name','','T') # get all the blank location names from data file
hdata=pmag.get_dictitem(data,'hysteresis_bcr','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_mr_moment','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_ms_moment','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_bc','','F') # there are data for a dayplot
if len(hdata)>0:
print 'dayplot_magic.py -sav -fmt '+fmt
os.system('dayplot_magic.py -sav -fmt '+fmt)
#if 'er_sites.txt' in filelist: # start with measurement data
# print 'working on er_sites'
#os.system('basemap_magic.py -sav -fmt '+fmt)
if 'rmag_anisotropy.txt' in filelist: # do anisotropy plots if possible
print 'working on rmag_anisotropy'
data,file_type=pmag.magic_read('rmag_anisotropy.txt') # read in data
if loc == './': data=pmag.get_dictitem(data,'er_location_name','','T') # get all the blank location names from data file
sdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','-1','T') # get specimen coordinates
gdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','0','T') # get specimen coordinates
tdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','100','T') # get specimen coordinates
if len(sdata)>3:
print 'aniso_magic.py -x -B -crd s -sav -fmt '+fmt
os.system('aniso_magic.py -x -B -crd s -sav -fmt '+fmt)
if len(gdata)>3:
os.system('aniso_magic.py -x -B -crd g -sav -fmt '+fmt)
if len(tdata)>3:
os.system('aniso_magic.py -x -B -crd t -sav -fmt '+fmt)
if loc!='./':os.chdir('..') # change working directories to each location
def main():
"""
NAME
odp_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
odp_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num = pmag.get_version()
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
ErSpecs, ErSamps, ErSites, ErLocs, ErCits = [], [], [], [], []
MagRecs = []
citation = "This study"
dir_path, demag = '.', 'NRM'
args = sys.argv
noave = 0
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-A" in args: noave = 1
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = dir_path + '/' + args[ind + 1]
ErSamps, file_type = pmag.magic_read(samp_file)
else:
samp_file = dir_path + '/' + samp_file
if '-LP' in args:
ind = args.index("-LP")
codelist = args[ind + 1]
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
if '-dc' not in args: methcode = "LT-AF-Z"
if '-dc' in args: methcode = "LT-AF-I"
if "T" in codes:
demag = "T"
if '-dc' not in args: methcode = "LT-T-Z"
if '-dc' in args: methcode = "LT-T-I"
if "I" in codes:
methcode = "LP-IRM"
if "S" in codes:
demag = "S"
methcode = "LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield = labfield
ans = input("DC lab field for ARM step: [50uT] ")
if ans == "":
arm_labfield = 50e-6
else:
arm_labfield = float(ans) * 1e-6
ans = input("temperature for total trm step: [600 C] ")
if ans == "":
trm_peakT = 600 + 273 # convert to kelvin
else:
trm_peakT = float(ans) + 273 # convert to kelvin
if "G" in codes: methcode = "LT-AF-G"
if "D" in codes: methcode = "LT-AF-D"
if "TRM" in codes:
demag = "T"
trm = 1
if demag == "T" and "ANI" in codes:
methcode = "LP-AN-TRM"
if demag == "AF" and "ANI" in codes:
methcode = "LP-AN-ARM"
if labfield == 0: labfield = 50e-6
if peakfield == 0: peakfield = .180
spec_file = dir_path + '/' + spec_file
site_file = dir_path + '/' + site_file
meas_file = dir_path + '/' + meas_file
filelist = os.listdir(dir_path) # read in list of files to import
specimens, samples, sites = [], [], []
MagRecs, SpecRecs, SampRecs = [], [], []
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower() == 'dsc':
print('processing: ', file)
MagRec, SpecRec, SampRec = {}, {}, {}
treatment_type, treatment_value, user = "", "", ""
inst = "ODP-SRM"
input = open(dir_path + '/' + file, 'r').readlines()
IDs = file.split('_') # splits on underscores
pieces = IDs[0].split('-')
expedition = pieces[0]
location = pieces[1]
if file[0] != '_':
while len(pieces[2]) < 4:
pieces[2] = '0' + pieces[2] # pad core to be 3 characters
specimen = ""
else:
specimen = "test"
for piece in pieces:
specimen = specimen + piece + '-'
specimen = specimen[:-1]
alt_spec = IDs[
1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name'] = expedition
SpecRec['er_location_name'] = location
SpecRec['er_site_name'] = specimen
SpecRec['er_sample_name'] = specimen
SpecRec['er_citation_names'] = citation
for key in list(SpecRec.keys()):
SampRec[key] = SpecRec[key]
SampRec['sample_azimuth'] = '0'
SampRec['sample_dip'] = '0'
SampRec['magic_method_codes'] = 'FS-C-DRILL-IODP:SP-SS-C:SO-V'
SpecRec['er_specimen_name'] = specimen
SampRec['er_specimen_names'] = specimen
for key in list(SpecRec.keys()):
MagRec[key] = SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names'] = user
MagRec['magic_method_codes'] = 'LT-NO'
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"] = 0.
MagRec["treatment_dc_field"] = '0'
MagRec["treatment_dc_field_phi"] = '0'
MagRec["treatment_dc_field_theta"] = '0'
MagRec["measurement_flag"] = 'g' # assume all data are "good"
MagRec["measurement_standard"] = 'u' # assume all data are "good"
MagRec["measurement_csd"] = '' # set csd to blank
SpecRec['er_specimen_alternatives'] = alt_spec
vol = 7e-6 # assume 7 cc samples
datestamp = input[1].split() # date time is second line of file
mmddyy = datestamp[0].split('/') # break into month day year
date = mmddyy[2] + ':' + mmddyy[0] + ":" + mmddyy[
1] + ':' + datestamp[1]
MagRec["measurement_date"] = date
for k in range(len(input)):
fields = input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type = "AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst = inst + ':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type = "ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst = inst + ':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type = "IRM"
if "treatment_value" in fields[0]:
values = fields[1].split(',')
value = values[0]
if value != " \n":
if treatment_type == "AF":
treatment_value = float(value) * 1e-3
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
elif treatment_type == "IRM":
treatment_value = float(value) * 1e-3
MagRec["treatment_dc_field"] = '%8.3e' % (
treatment_value) # IRM treat mT => T
if treatment_type == "ARM":
treatment_value = float(value) * 1e-3
dc_value = float(values[1]) * 1e-3
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"] = '%8.3e' % (
dc_value) # DC mT => T
if 'user' in fields[0]:
user = fields[-1]
MagRec["er_analyst_mail_names"] = user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"] = fields[-1]
MagRec[
"measurement_standard"] = 'u' # assume all data are "good"
if 'sample_area' in fields[0]:
vol = float(
fields[1]
) * 1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids'] = fields[
1] # run number is the LIMS measurement number
MagRec['external_database_names'] = 'LIMS'
if input[k][0:7] == '<MULTI>':
rec = input[k + 1].split(',') # list of data
for item in rec:
items = item.split('=')
if items[0].strip(
) == 'demag_level' and treatment_value == "":
treat = float(items[1])
if treat != 0:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':ODP-SRM-AF'
MagRec[
"treatment_ac_field"] = treat * 1e-3 # AF demag in treat mT => T
if items[0].strip() == 'inclination_w_tray_w_bkgrd':
MagRec['measurement_inc'] = items[1]
if items[0].strip() == 'declination_w_tray_w_bkgrd':
MagRec['measurement_dec'] = items[1]
if items[0].strip() == 'intensity_w_tray_w_bkgrd':
MagRec['measurement_magn_moment'] = '%8.3e' % (
float(items[1]) * vol
) # convert intensity from A/m to Am^2 using vol
if items[0].strip() == 'x_stdev':
MagRec['measurement_x_sd'] = items[1]
if items[0].strip() == 'y_stdev':
MagRec['measurement_y_sd'] = items[1]
if items[0].strip() == 'z_stdev':
MagRec['measurement_sd_z'] = items[1]
MagRec['magic_instrument_codes'] = inst
MagRec['measurement_number'] = '1'
MagRec['measurement_positions'] = ''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts = pmag.sort_diclist(MagRecs, 'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"] = '%8.3e' % (MagRec["treatment_ac_field"]
) # convert to string
pmag.magic_write(spec_file, SpecRecs, 'er_specimens')
if len(SampRecs) > 0:
SampOut, keys = pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file, SampOut, 'er_samples')
print('samples stored in ', samp_file)
pmag.magic_write(samp_file, SampRecs, 'er_samples')
print('specimens stored in ', spec_file)
Fixed = pmag.measurements_methods(MagOuts, noave)
pmag.magic_write(meas_file, Fixed, 'magic_measurements')
print('data stored in ', meas_file)
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
in_file, dir_path = 'magic_measurements.txt', '.'
if len(sys.argv) > 1:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv: norm = 0 # don't normalize
if '-sav' in sys.argv: plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
in_file = dir_path + '/' + in_file
print(in_file)
PmagRecs, file_type = pmag.magic_read(in_file)
if file_type != "magic_measurements":
print('bad input file')
sys.exit()
PmagRecs = pmag.get_dictitem(PmagRecs, 'magic_method_codes', 'LP-IRM-3D',
'has') # get all 3D IRM records
if len(PmagRecs) == 0:
print('no records found')
sys.exit()
specs = pmag.get_dictkey(PmagRecs, 'er_specimen_name', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, 'er_specimen_name', spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([
float(dat['measurement_dec']),
float(dat['measurement_inc']),
float(dat['measurement_magn_moment'])
])
Temps.append(float(dat['treatment_temp']) - 273.)
carts = pmag.dir2cart(DIMs).transpose()
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
hysteresis_magic.py
DESCRIPTION
calculates hystereis parameters and saves them in 3.0 specimen format file
makes plots if option selected
SYNTAX
hysteresis_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is agm_measurements.txt
-F: specify specimens.txt output file
-P: do not make the plots
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args=sys.argv
PLT=1
plots=0
fmt=pmag.get_named_arg_from_sys('-fmt','svg')
dir_path=pmag.get_named_arg_from_sys('-WD','.')
dir_path=os.path.realpath(dir_path)
verbose=pmagplotlib.verbose
version_num=pmag.get_version()
user=pmag.get_named_arg_from_sys('-usr','')
if "-h" in args:
print(main.__doc__)
sys.exit()
meas_file=pmag.get_named_arg_from_sys('-f','agm_measurements.txt')
spec_file=pmag.get_named_arg_from_sys('-F','specimens.txt')
if '-P' in args:
PLT=0
irm_init,imag_init=-1,-1
if '-sav' in args:
verbose=0
plots=1
pltspec=pmag.get_named_arg_from_sys('-spc',0)
if pltspec:
#pltspec= args[ind+1]
verbose=0
plots=1
spec_file=dir_path+'/'+spec_file
meas_file=dir_path+'/'+meas_file
SpecRecs=[]
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type!='measurements':
print(main.__doc__)
print('bad file')
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs,RemRecs=[],[]
HDD={}
if verbose:
if verbose and PLT:print("Plots may be on top of each other - use mouse to place ")
if PLT:
HDD['hyst'],HDD['deltaM'],HDD['DdeltaM']=1,2,3
pmagplotlib.plot_init(HDD['DdeltaM'],5,5)
pmagplotlib.plot_init(HDD['deltaM'],5,5)
pmagplotlib.plot_init(HDD['hyst'],5,5)
imag_init=0
irm_init=0
else:
HDD['hyst'],HDD['deltaM'],HDD['DdeltaM'],HDD['irm'],HDD['imag']=0,0,0,0,0
#
if spec_file: prior_data,file_type=pmag.magic_read(spec_file)
#
# get list of unique experiment names and specimen names
#
experiment_names,sids=[],[]
hys_data=pmag.get_dictitem(meas_data,'method_codes','LP-HYS','has')
dcd_data=pmag.get_dictitem(meas_data,'method_codes','LP-IRM-DCD','has')
imag_data=pmag.get_dictitem(meas_data,'method_codes','LP-IMAG','has')
for rec in hys_data:
if rec['experiment'] not in experiment_names:experiment_names.append(rec['experiment'])
if rec['specimen'] not in sids:sids.append(rec['specimen'])
#
k=0
if pltspec:
k=sids.index(pltspec)
print(sids[k])
while k < len(sids):
specimen=sids[k]
HystRec={'specimen':specimen,'experiment':""} # initialize a new specimen hysteresis record
if verbose and PLT:print(specimen, k+1 , 'out of ',len(sids))
#
#
B,M,Bdcd,Mdcd=[],[],[],[] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
Bimag,Mimag=[],[] #Bimag,Mimag for initial magnetization curves
spec_data=pmag.get_dictitem(hys_data,'specimen',specimen,'T') # fish out all the LP-HYS data for this specimen
if len(spec_data)>0:
meths=spec_data[0]['method_codes'].split(':')
e=spec_data[0]['experiment']
HystRec['experiment']=spec_data[0]['experiment']
for rec in spec_data:
B.append(float(rec['meas_field_dc']))
M.append(float(rec['magn_moment']))
spec_data=pmag.get_dictitem(dcd_data,'specimen',specimen,'T') # fish out all the data for this specimen
if len(spec_data)>0:
HystRec['experiment']=HystRec['experiment']+':'+spec_data[0]['experiment']
irm_exp=spec_data[0]['experiment']
for rec in spec_data:
Bdcd.append(float(rec['treat_dc_field']))
Mdcd.append(float(rec['magn_moment']))
spec_data=pmag.get_dictitem(imag_data,'specimen',specimen,'T') # fish out all the data for this specimen
if len(spec_data)>0:
imag_exp=spec_data[0]['experiment']
for rec in spec_data:
Bimag.append(float(rec['meas_field_dc']))
Mimag.append(float(rec['magn_moment']))
#
# now plot the hysteresis curve
#
if len(B)>0:
hmeths=[]
for meth in meths: hmeths.append(meth)
hpars=pmagplotlib.plotHDD(HDD,B,M,e)
if verbose and PLT:pmagplotlib.drawFIGS(HDD)
#
if verbose:pmagplotlib.plotHPARS(HDD,hpars,'bs')
HystRec['hyst_mr_moment']=hpars['hysteresis_mr_moment']
HystRec['hyst_ms_moment']=hpars['hysteresis_ms_moment']
HystRec['hyst_bc']=hpars['hysteresis_bc']
HystRec['hyst_bcr']=hpars['hysteresis_bcr']
HystRec['susc_h']=hpars['hysteresis_xhf']
HystRec['experiments']=e
HystRec['software_packages']=version_num
if hpars["magic_method_codes"] not in hmeths:hmeths.append(hpars["magic_method_codes"])
methods=""
for meth in hmeths:
methods=methods+meth.strip()+":"
HystRec["method_codes"]=methods[:-1]
HystRec["citations"]="This study"
#
if len(Bdcd)>0:
rmeths=[]
for meth in meths: rmeths.append(meth)
if verbose and PLT:print('plotting IRM')
if irm_init==0:
HDD['irm']=5
pmagplotlib.plot_init(HDD['irm'],5,5)
irm_init=1
rpars=pmagplotlib.plotIRM(HDD['irm'],Bdcd,Mdcd,irm_exp)
HystRec['rem_mr_moment']=rpars['remanence_mr_moment']
HystRec['rem_bcr']=rpars['remanence_bcr']
HystRec['experiments']=specimen+':'+irm_exp
if rpars["magic_method_codes"] not in meths:meths.append(rpars["magic_method_codes"])
methods=""
for meth in rmeths:
methods=methods+meth.strip()+":"
HystRec["method_codes"]=HystRec['method_codes']+':'+methods[:-1]
HystRec["citations"]="This study"
else:
if irm_init:pmagplotlib.clearFIG(HDD['irm'])
if len(Bimag)>0:
if verbose and PLT:print('plotting initial magnetization curve')
# first normalize by Ms
Mnorm=[]
for m in Mimag: Mnorm.append(old_div(m,float(hpars['hysteresis_ms_moment'])))
if imag_init==0:
HDD['imag']=4
pmagplotlib.plot_init(HDD['imag'],5,5)
imag_init=1
pmagplotlib.plotIMAG(HDD['imag'],Bimag,Mnorm,imag_exp)
else:
if imag_init:pmagplotlib.clearFIG(HDD['imag'])
if len(list(HystRec.keys()))>0:HystRecs.append(HystRec)
#
files={}
if plots:
if pltspec:s=pltspec
files={}
for key in list(HDD.keys()):
files[key]=s+'_'+key+'.'+fmt
pmagplotlib.saveP(HDD,files)
if pltspec:sys.exit()
if verbose and PLT:
pmagplotlib.drawFIGS(HDD)
ans=input("S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n ")
if ans=="a":
files={}
for key in list(HDD.keys()):
files[key]=specimen+'_'+key+'.'+fmt
pmagplotlib.saveP(HDD,files)
if ans=='':k+=1
if ans=="p":
del HystRecs[-1]
k-=1
if ans=='q':
print("Good bye")
sys.exit()
if ans=='s':
keepon=1
specimen=input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
k =sids.index(specimen)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if specimen in sids[qq]:tmplist.append(sids[qq])
print(specimen," not found, but this was: ")
print(tmplist)
specimen=input('Select one or try again\n ')
k =sids.index(specimen)
else:
k+=1
if len(B)==0 and len(Bdcd)==0:
if verbose:print('skipping this one - no hysteresis data')
k+=1
if len(HystRecs)>0:
# go through prior_data, clean out prior results and save combined file as spec_file
SpecRecs,keys=[],list(HystRecs[0].keys())
if len(prior_data)>0:
prior_keys=list(prior_data[0].keys())
else: prior_keys=[]
for rec in prior_data:
for key in keys:
if key not in list(rec.keys()):rec[key]=""
if 'LP-HYS' not in rec['method_codes']:
SpecRecs.append(rec)
for rec in HystRecs:
for key in prior_keys:
if key not in list(rec.keys()):rec[key]=""
prior=pmag.get_dictitem(prior_data,'specimen',rec['specimen'],'T')
if len(prior)>0 and 'sample' in list(prior[0].keys()):
rec['sample']=prior[0]['sample'] # pull sample name from prior specimens table
SpecRecs.append(rec)
pmag.magic_write(spec_file,SpecRecs,"specimens")
if verbose:print("hysteresis parameters saved in ",spec_file)
def main():
"""
NAME
hysteresis_magic.py
DESCRIPTION
calculates hystereis parameters and saves them in rmag_hystereis format file
makes plots if option selected
SYNTAX
hysteresis_magic.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specify input file, default is agm_measurements.txt
-fh: specify rmag_hysteresis.txt input file
-F: specify output file, default is rmag_hysteresis.txt
-P: do not make the plots
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
PLT = 1
plots = 0
user, meas_file, rmag_out, rmag_file = "", "agm_measurements.txt", "rmag_hysteresis.txt", ""
pltspec = ""
dir_path = '.'
fmt = 'svg'
verbose = pmagplotlib.verbose
version_num = pmag.get_version()
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-f' in args:
ind = args.index("-f")
meas_file = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
rmag_out = args[ind + 1]
if '-fh' in args:
ind = args.index("-fh")
rmag_file = args[ind + 1]
rmag_file = dir_path + '/' + rmag_file
if '-P' in args:
PLT = 0
irm_init, imag_init = -1, -1
if '-sav' in args:
verbose = 0
plots = 1
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind + 1]
verbose = 0
plots = 1
if '-fmt' in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
rmag_out = dir_path + '/' + rmag_out
meas_file = dir_path + '/' + meas_file
rmag_rem = dir_path + "/rmag_remanence.txt"
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print main.__doc__
print 'bad file'
sys.exit()
#
# initialize some variables
# define figure numbers for hyst,deltaM,DdeltaM curves
HystRecs, RemRecs = [], []
HDD = {}
if verbose:
if verbose and PLT:
print "Plots may be on top of each other - use mouse to place "
if PLT:
HDD['hyst'], HDD['deltaM'], HDD['DdeltaM'] = 1, 2, 3
pmagplotlib.plot_init(HDD['DdeltaM'], 5, 5)
pmagplotlib.plot_init(HDD['deltaM'], 5, 5)
pmagplotlib.plot_init(HDD['hyst'], 5, 5)
imag_init = 0
irm_init = 0
else:
HDD['hyst'], HDD['deltaM'], HDD['DdeltaM'], HDD['irm'], HDD[
'imag'] = 0, 0, 0, 0, 0
#
if rmag_file != "": hyst_data, file_type = pmag.magic_read(rmag_file)
#
# get list of unique experiment names and specimen names
#
experiment_names, sids = [], []
for rec in meas_data:
meths = rec['magic_method_codes'].split(':')
methods = []
for meth in meths:
methods.append(meth.strip())
if 'LP-HYS' in methods:
if 'er_synthetic_name' in rec.keys(
) and rec['er_synthetic_name'] != "":
rec['er_specimen_name'] = rec['er_synthetic_name']
if rec['magic_experiment_name'] not in experiment_names:
experiment_names.append(rec['magic_experiment_name'])
if rec['er_specimen_name'] not in sids:
sids.append(rec['er_specimen_name'])
#
k = 0
locname = ''
if pltspec != "":
k = sids.index(pltspec)
print sids[k]
while k < len(sids):
s = sids[k]
if verbose and PLT: print s, k + 1, 'out of ', len(sids)
#
#
B, M, Bdcd, Mdcd = [], [], [], [
] #B,M for hysteresis, Bdcd,Mdcd for irm-dcd data
Bimag, Mimag = [], [] #Bimag,Mimag for initial magnetization curves
first_dcd_rec, first_rec, first_imag_rec = 1, 1, 1
for rec in meas_data:
methcodes = rec['magic_method_codes'].split(':')
meths = []
for meth in methcodes:
meths.append(meth.strip())
if rec['er_specimen_name'] == s and "LP-HYS" in meths:
B.append(float(rec['measurement_lab_field_dc']))
M.append(float(rec['measurement_magn_moment']))
if first_rec == 1:
e = rec['magic_experiment_name']
HystRec = {}
first_rec = 0
if "er_location_name" in rec.keys():
HystRec["er_location_name"] = rec["er_location_name"]
locname = rec['er_location_name'].replace('/', '-')
if "er_sample_name" in rec.keys():
HystRec["er_sample_name"] = rec["er_sample_name"]
if "er_site_name" in rec.keys():
HystRec["er_site_name"] = rec["er_site_name"]
if "er_synthetic_name" in rec.keys(
) and rec['er_synthetic_name'] != "":
HystRec["er_synthetic_name"] = rec["er_synthetic_name"]
else:
HystRec["er_specimen_name"] = rec["er_specimen_name"]
if rec['er_specimen_name'] == s and "LP-IRM-DCD" in meths:
Bdcd.append(float(rec['treatment_dc_field']))
Mdcd.append(float(rec['measurement_magn_moment']))
if first_dcd_rec == 1:
RemRec = {}
irm_exp = rec['magic_experiment_name']
first_dcd_rec = 0
if "er_location_name" in rec.keys():
RemRec["er_location_name"] = rec["er_location_name"]
if "er_sample_name" in rec.keys():
RemRec["er_sample_name"] = rec["er_sample_name"]
if "er_site_name" in rec.keys():
RemRec["er_site_name"] = rec["er_site_name"]
if "er_synthetic_name" in rec.keys(
) and rec['er_synthetic_name'] != "":
RemRec["er_synthetic_name"] = rec["er_synthetic_name"]
else:
RemRec["er_specimen_name"] = rec["er_specimen_name"]
if rec['er_specimen_name'] == s and "LP-IMAG" in meths:
if first_imag_rec == 1:
imag_exp = rec['magic_experiment_name']
first_imag_rec = 0
Bimag.append(float(rec['measurement_lab_field_dc']))
Mimag.append(float(rec['measurement_magn_moment']))
#
# now plot the hysteresis curve
#
if len(B) > 0:
hmeths = []
for meth in meths:
hmeths.append(meth)
hpars = pmagplotlib.plotHDD(HDD, B, M, e)
if verbose and PLT: pmagplotlib.drawFIGS(HDD)
#
# get prior interpretations from hyst_data
if rmag_file != "":
hpars_prior = {}
for rec in hyst_data:
if rec['magic_experiment_names'] == e:
if rec['hysteresis_bcr'] != "" and rec[
'hysteresis_mr_moment'] != "":
hpars_prior['hysteresis_mr_moment'] = rec[
'hysteresis_mr_moment']
hpars_prior['hysteresis_ms_moment'] = rec[
'hysteresis_ms_moment']
hpars_prior['hysteresis_bc'] = rec['hysteresis_bc']
hpars_prior['hysteresis_bcr'] = rec[
'hysteresis_bcr']
break
if verbose: pmagplotlib.plotHPARS(HDD, hpars_prior, 'ro')
else:
if verbose: pmagplotlib.plotHPARS(HDD, hpars, 'bs')
HystRec['hysteresis_mr_moment'] = hpars['hysteresis_mr_moment']
HystRec['hysteresis_ms_moment'] = hpars['hysteresis_ms_moment']
HystRec['hysteresis_bc'] = hpars['hysteresis_bc']
HystRec['hysteresis_bcr'] = hpars['hysteresis_bcr']
HystRec['hysteresis_xhf'] = hpars['hysteresis_xhf']
HystRec['magic_experiment_names'] = e
HystRec['magic_software_packages'] = version_num
if hpars["magic_method_codes"] not in hmeths:
hmeths.append(hpars["magic_method_codes"])
methods = ""
for meth in hmeths:
methods = methods + meth.strip() + ":"
HystRec["magic_method_codes"] = methods[:-1]
HystRec["er_citation_names"] = "This study"
HystRecs.append(HystRec)
#
if len(Bdcd) > 0:
rmeths = []
for meth in meths:
rmeths.append(meth)
if verbose and PLT: print 'plotting IRM'
if irm_init == 0:
HDD['irm'] = 5
pmagplotlib.plot_init(HDD['irm'], 5, 5)
irm_init = 1
rpars = pmagplotlib.plotIRM(HDD['irm'], Bdcd, Mdcd, irm_exp)
RemRec['remanence_mr_moment'] = rpars['remanence_mr_moment']
RemRec['remanence_bcr'] = rpars['remanence_bcr']
RemRec['magic_experiment_names'] = irm_exp
if rpars["magic_method_codes"] not in meths:
meths.append(rpars["magic_method_codes"])
methods = ""
for meth in rmeths:
methods = methods + meth.strip() + ":"
RemRec["magic_method_codes"] = methods[:-1]
RemRec["er_citation_names"] = "This study"
RemRecs.append(RemRec)
else:
if irm_init: pmagplotlib.clearFIG(HDD['irm'])
if len(Bimag) > 0:
if verbose: print 'plotting initial magnetization curve'
# first normalize by Ms
Mnorm = []
for m in Mimag:
Mnorm.append(m / float(hpars['hysteresis_ms_moment']))
if imag_init == 0:
HDD['imag'] = 4
pmagplotlib.plot_init(HDD['imag'], 5, 5)
imag_init = 1
pmagplotlib.plotIMAG(HDD['imag'], Bimag, Mnorm, imag_exp)
else:
if imag_init: pmagplotlib.clearFIG(HDD['imag'])
#
files = {}
if plots:
if pltspec != "": s = pltspec
files = {}
for key in HDD.keys():
files[key] = locname + '_' + s + '_' + key + '.' + fmt
pmagplotlib.saveP(HDD, files)
if pltspec != "": sys.exit()
if verbose and PLT:
pmagplotlib.drawFIGS(HDD)
ans = raw_input(
"S[a]ve plots, [s]pecimen name, [q]uit, <return> to continue\n "
)
if ans == "a":
files = {}
for key in HDD.keys():
files[key] = locname + '_' + s + '_' + key + '.' + fmt
pmagplotlib.saveP(HDD, files)
if ans == '': k += 1
if ans == "p":
del HystRecs[-1]
k -= 1
if ans == 'q':
print "Good bye"
sys.exit()
if ans == 's':
keepon = 1
specimen = raw_input(
'Enter desired specimen name (or first part there of): ')
while keepon == 1:
try:
k = sids.index(specimen)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if specimen in sids[qq]: tmplist.append(sids[qq])
print specimen, " not found, but this was: "
print tmplist
specimen = raw_input('Select one or try again\n ')
k = sids.index(specimen)
else:
k += 1
if len(B) == 0 and len(Bdcd) == 0:
if verbose: print 'skipping this one - no hysteresis data'
k += 1
if rmag_out == "" and ans == 's' and verbose:
really = raw_input(
" Do you want to overwrite the existing rmag_hystersis.txt file? 1/[0] "
)
if really == "":
print 'i thought not - goodbye'
sys.exit()
rmag_out = "rmag_hysteresis.txt"
if len(HystRecs) > 0:
pmag.magic_write(rmag_out, HystRecs, "rmag_hysteresis")
if verbose: print "hysteresis parameters saved in ", rmag_out
if len(RemRecs) > 0:
pmag.magic_write(rmag_rem, RemRecs, "rmag_remanence")
if verbose: print "remanence parameters saved in ", rmag_rem
def main():
"""
NAME
strip_magic.py
DESCRIPTION
plots various parameters versus depth or age
SYNTAX
strip_magic.py [command line optins]
OPTIONS
-h prints help message and quits
-DM NUM: specify data model num, options 2 (legacy) or 3 (default)
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[pmag_specimens, pmag_samples, pmag_sites, pmag_results, magic_web]
-obj [sit,sam,all]: specify object to site,sample,all for pmag_result table, default is all
-fmt [svg,png,jpg], format for images - default is svg
-x [age,pos]: specify whether age or stratigraphic position
-y [dec,inc,int,chi,lat,lon,vdm,vadm]
(lat and lon are VGP lat and lon)
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04]
-mcd method_code, specify method code, default is first one encountered
-sav save plot and quit
NOTES
when x and/or y are not specified, a list of possibilities will be presented to the user for choosing
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
xaxis, xplotind, yplotind = "", 0, 0 # (0 for strat pos)
yaxis, Xinc = "", ""
plot = 0
obj = 'all'
data_model_num = int(pmag.get_named_arg("-DM", 3))
# 2.5 keys
if data_model_num == 2:
supported = [
'pmag_specimens', 'pmag_samples', 'pmag_sites', 'pmag_results',
'magic_web'
] # available file types
Depth_keys = [
'specimen_core_depth', 'specimen_height', 'specimen_elevation',
'specimen_composite_depth', 'sample_core_depth', 'sample_height',
'sample_elevation', 'sample_composite_depth', 'site_core_depth',
'site_height', 'site_elevation', 'site_composite_depth',
'average_height'
]
Age_keys = [
'specimen_inferred_age', 'sample_inferred_age',
'site_inferred_age', 'average_age'
]
Unit_keys = {
'specimen_inferred_age': 'specimen_inferred_age_unit',
'sample_inferred_age': 'sample_inferred_age_unit',
'site_inferred_age': 'site_inferred_age_unit',
'average_age': 'average_age_unit'
}
Dec_keys = [
'measurement_dec', 'specimen_dec', 'sample_dec', 'site_dec',
'average_dec'
]
Inc_keys = [
'measurement_inc', 'specimen_inc', 'sample_inc', 'site_inc',
'average_inc'
]
Int_keys = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass', 'specimen_int',
'specimen_int_rel', 'sample_int', 'sample_int_rel', 'site_int',
'site_int_rel', 'average_int', 'average_int_rel'
]
Chi_keys = ['measurement_chi_volume', 'measurement_chi_mass']
Lat_keys = ['sample_lat', 'site_lat', 'average_lat']
VLat_keys = ['vgp_lat']
VLon_keys = ['vgp_lon']
Vdm_keys = ['vdm']
Vadm_keys = ['vadm']
method_col_name = "magic_method_codes"
else:
# 3.0 keys
supported = ["specimens", "samples", "sites",
"locations"] # available file types
Depth_keys = ["height", "core_depth", "elevation", "composite_depth"]
Age_keys = ["age"]
Unit_keys = {"age": "age"}
Chi_keys = ["susc_chi_volume", "susc_chi_mass"]
Int_keys = [
"magn_moment", "magn_volume", "magn_mass", "int_abs", "int_rel"
]
Inc_keys = ["dir_inc"]
Dec_keys = ["dir_dec"]
Lat_Keys = ["lat"]
VLat_keys = ["vgp_lat", "pole_lat"]
VLon_keys = ["vgp_lon", "pole_lon"]
Vdm_keys = ["vdm", "pdm"]
Vadm_keys = ["vadm", "padm"]
method_col_name = "method_codes"
#
X_keys = [Age_keys, Depth_keys]
Y_keys = [
Dec_keys, Inc_keys, Int_keys, Chi_keys, VLat_keys, VLon_keys, Vdm_keys,
Vadm_keys
]
method, fmt = "", 'svg'
FIG = {'strat': 1}
plotexp, pTS = 0, 0
dir_path = pmag.get_named_arg("-WD", ".")
# default files
if data_model_num == 3:
res_file = pmag.get_named_arg("-f", "sites.txt")
else:
res_file = pmag.get_named_arg("-f", "pmag_results.txt")
res_file = pmag.resolve_file_name(res_file, dir_path)
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
obj = sys.argv[ind + 1]
if '-x' in sys.argv:
ind = sys.argv.index('-x')
xaxis = sys.argv[ind + 1]
if '-y' in sys.argv:
ind = sys.argv.index('-y')
yaxis = sys.argv[ind + 1]
if yaxis == 'dec':
ykeys = Dec_keys
if yaxis == 'inc':
ykeys = Inc_keys
if yaxis == 'int':
ykeys = Int_keys
if yaxis == 'chi':
ykeys = Chi_keys
if yaxis == 'lat':
ykeys = VLat_keys
if yaxis == 'lon':
ykeys = VLon_keys
if yaxis == 'vdm':
ykeys = Vdm_keys
if yaxis == 'vadm':
ykeys = Vadm_keys
if '-mcd' in sys.argv:
ind = sys.argv.index('-mcd')
method = sys.argv[ind + 1]
if '-ts' in sys.argv:
ind = sys.argv.index('-ts')
ts = sys.argv[ind + 1]
amin = float(sys.argv[ind + 2])
amax = float(sys.argv[ind + 3])
pTS = 1
if '-Iex' in sys.argv:
plotexp = 1
if '-sav' in sys.argv:
plot = 1
#
#
# get data read in
Results, file_type = pmag.magic_read(res_file)
if file_type not in supported:
print("Unsupported file type ({}), try again".format(file_type))
sys.exit()
PltObjs = ['all']
if data_model_num == 2:
if file_type == 'pmag_results': # find out what to plot
for rec in Results:
resname = rec['pmag_result_name'].split()
if 'Sample' in resname and 'sam' not in PltObjs:
PltObjs.append('sam')
if 'Site' in resname and 'sit' not in PltObjs:
PltObjs.append('sit')
methcodes = []
# need to know all the measurement types from method_codes
if "magic_method_codes" in list(Results[0].keys()):
for rec in Results:
meths = rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in methcodes and 'LP' in meth:
# look for the lab treatments
methcodes.append(meth.strip())
#
# initialize some variables
X_unit = "" # Unit for age or depth plotting (meters if depth)
Xplots, Yplots = [], []
Xunits = []
yplotind, xplotind = 0, 0
#
# step through possible plottable keys
#
if xaxis == "" or yaxis == "":
for key in list(Results[0].keys()):
for keys in X_keys:
for xkeys in keys:
if key in xkeys:
for ResRec in Results:
if ResRec[key] != "":
# only plot something if there is something to plot!
Xplots.append(key)
break
for keys in Y_keys:
for pkeys in keys:
if key in pkeys:
for ResRec in Results:
if ResRec[key] != "":
Yplots.append(key)
break
X, Y = [], []
for plt in Xplots:
if plt in Age_keys and 'age' not in X:
X.append('age')
if plt in Depth_keys and 'pos' not in X:
X.append('pos')
for plt in Yplots:
if plt in Dec_keys and 'dec' not in Y:
Y.append('dec')
if plt in Inc_keys and 'inc' not in Y:
Y.append('inc')
if plt in Int_keys and 'int' not in Y:
Y.append('int')
if plt in Chi_keys and 'chi' not in Y:
Y.append('chi')
if plt in VLat_keys and 'lat' not in Y:
Y.append('lat')
if plt in VLon_keys and 'lon' not in Y:
Y.append('lon')
if plt in Vadm_keys and 'vadm' not in Y:
Y.append('vadm')
if plt in Vdm_keys and 'vdm' not in Y:
Y.append('vdm')
if file_type == 'pmag_results':
print('available objects for plotting: ', PltObjs)
print('available X plots: ', X)
print('available Y plots: ', Y)
print('available method codes: ', methcodes)
f = open(dir_path + '/.striprc', 'w')
for x in X:
f.write('x:' + x + '\n')
for y in Y:
f.write('y:' + y + '\n')
for m in methcodes:
f.write('m:' + m + '\n')
for obj in PltObjs:
f.write('obj:' + obj + '\n')
sys.exit()
if plotexp == 1:
for lkey in Lat_keys:
for key in list(Results[0].keys()):
if key == lkey:
lat = float(Results[0][lkey])
Xinc = [pmag.pinc(lat), -pmag.pinc(lat)]
break
if Xinc == "":
print('can not plot expected inc for site - lat unknown')
if method != "" and method not in methcodes:
print('your method not available, but these are: ')
print(methcodes)
print('use ', methcodes[0], '? ^D to quit')
if xaxis == 'age':
for akey in Age_keys:
for key in list(Results[0].keys()):
if key == akey:
Xplots.append(key)
Xunits.append(Unit_keys[key])
if xaxis == 'pos':
for dkey in Depth_keys:
for key in list(Results[0].keys()):
if key == dkey:
Xplots.append(key)
if len(Xplots) == 0:
print('desired X axis information not found')
sys.exit()
if xaxis == 'age':
age_unit = Results[0][Xunits[0]]
if len(Xplots) > 1:
print('multiple X axis keys found, using: ', Xplots[xplotind])
for ykey in ykeys:
for key in list(Results[0].keys()):
if key == ykey:
Yplots.append(key)
if len(Yplots) == 0:
print('desired Y axis information not found')
sys.exit()
if len(Yplots) > 1:
print('multiple Y axis keys found, using: ', Yplots[yplotind])
# check if age or depth info
if len(Xplots) == 0:
print("Must have either age or height info to plot ")
sys.exit()
#
# check for variable to plot
#
#
# determine X axis (age or depth)
#
if xaxis == "age":
plotind = "1"
if method == "":
try:
method = methcodes[0]
except IndexError:
method = ""
if xaxis == 'pos':
xlab = "Stratigraphic Height (meters)"
else:
xlab = "Age (" + age_unit + ")"
Xkey = Xplots[xplotind]
Ykey = Yplots[yplotind]
ylab = Ykey
#
# collect the data for plotting
XY = []
isign = 1.
# if float(Results[0][Xkey])/float(Results[-1][Xkey])>0 and float(Results[0][Xkey])<0:
# isign=-1. # x axis all same sign and negative, take positive (e.g.,for depth in core)
# xlab="Stratigraphic Position (meters)"
# else:
# isign=1.
for rec in Results:
if "magic_method_codes" in list(rec.keys()):
meths = rec["magic_method_codes"].split(":")
if method in meths: # make sure it is desired lab treatment step
if obj == 'all' and rec[Xkey].strip() != "":
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
elif rec[Xkey].strip() != "":
name = rec['pmag_result_name'].split()
if obj == 'sit' and "Site" in name:
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
if obj == 'sam' and "Sample" in name:
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
elif method == "":
if obj == 'all' and rec[Xkey].strip() != "":
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
elif rec[Xkey].strip() != "":
name = rec['pmag_result_name'].split()
if obj == 'sit' and "Site" in name:
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
if obj == 'sam' and "Sample" in name:
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
else:
print("Something wrong with your plotting choices")
break
XY.sort()
title = ""
if "er_locations_names" in list(Results[0].keys()):
title = Results[0]["er_location_names"]
if "er_locations_name" in list(Results[0].keys()):
title = Results[0]["er_location_name"]
labels = [xlab, ylab, title]
pmagplotlib.plot_init(FIG['strat'], 10, 5)
pmagplotlib.plot_strat(FIG['strat'], XY, labels) # plot them
if plotexp == 1:
pmagplotlib.plot_hs(FIG['strat'], Xinc, 'b', '--')
if yaxis == 'inc' or yaxis == 'lat':
pmagplotlib.plot_hs(FIG['strat'], [0], 'b', '-')
pmagplotlib.plot_hs(FIG['strat'], [-90, 90], 'g', '-')
if pTS == 1:
FIG['ts'] = 2
pmagplotlib.plot_init(FIG['ts'], 10, 5)
pmagplotlib.plot_ts(FIG['ts'], [amin, amax], ts)
files = {}
for key in list(FIG.keys()):
files[key] = key + '.' + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
files = {}
files['strat'] = xaxis + '_' + yaxis + '_.' + fmt
files['ts'] = 'ts.' + fmt
titles = {}
titles['strat'] = 'Depth/Time Series Plot'
titles['ts'] = 'Time Series Plot'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 1:
pmagplotlib.save_plots(FIG, files)
else:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, [q]uit without saving: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
lsq_redo.py
DESCRIPTION
converts a tab delimited LSQ format to PmagPy redo file and edits the magic_measurements table to mark "bad" measurements.
SYNTAX
lsq_redo.py [-h] [command line options]
OPTIONS
-h: prints help message and quits
-f FILE: specify LSQ input file
-fm MFILE: specify measurements file for editting, default is
magic_measurements.txt
-F FILE: specify output file, default is 'zeq_redo'
"""
letters = string.ascii_uppercase
for l in string.ascii_lowercase:
letters = letters + l
dir_path = '.'
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
inspec = dir_path + '/' + sys.argv[ind + 1]
else:
zfile = dir_path + '/zeq_redo'
if '-fm' in sys.argv:
ind = sys.argv.index('-f')
meas_file = dir_path + '/' + sys.argv[ind + 1]
else:
meas_file = dir_path + '/magic_measurements.txt'
if '-F' in sys.argv:
ind = sys.argv.index('-F')
zfile = dir_path + '/' + sys.argv[ind + 1]
else:
zfile = dir_path + '/zeq_redo'
try:
open(meas_file, "r")
meas_data, file_type = pmag.magic_read(meas_file)
except IOError:
print(main.__doc__)
print("""You must have a valid measurements file prior to converting
this LSQ file""")
sys.exit()
zredo = open(zfile, "w")
MeasRecs = []
#
# read in LSQ file
#
specs, MeasOuts = [], []
prior_spec_data = open(inspec, 'r').readlines()
for line in prior_spec_data:
if len(line) < 2:
sys.exit()
# spec=line[0:14].strip().replace(" ","") # get out the specimen name = collapsing spaces
# rec=line[14:].split() # split up the rest of the line
rec = line.split('\t')
spec = rec[0].lower()
specs.append(spec)
comp_name = rec[2] # assign component name
calculation_type = "DE-FM"
if rec[1][0] == "L":
calculation_type = "DE-BFL" # best-fit line
else:
calculation_type = "DE-BFP" # best-fit line
lists = rec[7].split('-') # get list of data used
incl = []
for l in lists[0]:
incl.append(letters.index(l))
for l in letters[letters.index(lists[0][-1]) +
1:letters.index(lists[1][0])]:
incl.append(letters.index(l)) # add in the in between parts
for l in lists[1]:
incl.append(letters.index(l))
if len(lists) > 2:
for l in letters[letters.index(lists[1][-1]) +
1:letters.index(lists[2][0])]:
incl.append(letters.index(l)) # add in the in between parts
for l in lists[2]:
incl.append(letters.index(l))
# now find all the data for this specimen in measurements
datablock, min, max = [], "", ""
demag = 'N'
for s in meas_data:
if s['er_specimen_name'].lower() == spec.lower():
meths = s['magic_method_codes'].replace(" ", "").split(":")
if 'LT-NO' in meths or 'LT-AF-Z' in meths or 'LT-T-Z' in meths:
datablock.append(s)
if len(datablock) > 0:
for t in datablock:
print(t['magic_method_codes'])
incl_int = len(incl)
while incl[-1] > len(datablock) - 1:
del incl[
-1] # don't include measurements beyond what is in file
if len(incl) != incl_int:
'converting calculation type to best-fit line'
meths0 = datablock[incl[0]]['magic_method_codes'].replace(
" ", "").split(':')
meths1 = datablock[incl[-1]]['magic_method_codes'].replace(
" ", "").split(':')
H0 = datablock[incl[0]]['treatment_ac_field']
T0 = datablock[incl[0]]['treatment_temp']
H1 = datablock[incl[-1]]['treatment_ac_field']
T1 = datablock[incl[-1]]['treatment_temp']
if 'LT-T-Z' in meths1:
max = T1
demag = "T"
elif 'LT-AF-Z' in meths1:
demag = "AF"
max = H1
if 'LT-NO' in meths0:
if demag == 'T':
min = 273
else:
min = 0
elif 'LT-T-Z' in meths0:
min = T0
else:
min = H0
for ind in range(incl[0]):
MeasRecs.append(datablock[ind])
for ind in range(incl[0], incl[-1]):
if ind not in incl: # datapoint not used in calculation
datablock[ind]['measurement_flag'] = 'b'
MeasRecs.append(datablock[ind])
for ind in range(incl[-1], len(datablock)):
MeasRecs.append(datablock[ind])
outstring = '%s %s %s %s %s \n' % (spec, calculation_type, min,
max, comp_name)
zredo.write(outstring)
for s in meas_data: # collect the rest of the measurement data not already included
if s['er_specimen_name'] not in specs:
MeasRecs.append(s)
pmag.magic_write(meas_file, MeasRecs,
'magic_measurements') # write out annotated measurements
def main():
"""
NAME
microwave_magic.py
DESCRIPTION
plots microwave paleointensity data, allowing interactive setting of bounds.
Saves and reads interpretations
from a pmag_specimen formatted table, default: microwave_specimens.txt
SYNTAX
microwave_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set magic_measurements input file
-fsp PRIOR, set pmag_specimen prior interpretations file
-fcr CRIT, set criteria file for grading.
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (default format)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds adn quits
-b BEG END: sets bounds for calculation
BEG: starting step for slope calculation
END: ending step for slope calculation
DEFAULTS
MEAS: magic_measurements.txt
CRIT: NONE
PRIOR: microwave_specimens.txt
OUTPUT
figures:
ALL: numbers refer to temperature steps in command line window
1) Arai plot: closed circles are zero-field first/infield
open circles are infield first/zero-field
triangles are pTRM checks
squares are pTRM tail checks
VDS is vector difference sum
diamonds are bounds for interpretation
2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes
X rotated to NRM direction
3) (De/Re)Magnetization diagram:
circles are NRM remaining
squares are pTRM gained
command line window:
list is: temperature step numbers, power (J), Dec, Inc, Int (units of magic_measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates .svg format files with specimen_name, plot type as name
"""
#
# initializations
#
meas_file, critout, inspec = "magic_measurements.txt", "", "microwave_specimens.txt"
inlt = 0
version_num = pmag.get_version()
Tinit, DCZ, field, first_save = 0, 0, -1, 1
user, comment = "", ''
ans, specimen, recnum, start, end = 0, 0, 0, 0, 0
plots, pmag_out, samp_file, style = 0, "", "", "svg"
fmt = '.' + style
#
# default acceptance criteria
#
accept_keys = [
'specimen_int_ptrm_n', 'specimen_md', 'specimen_fvds',
'specimen_b_beta', 'specimen_dang', 'specimen_drats', 'specimen_Z'
]
accept = {}
accept['specimen_int_ptrm_n'] = 2
accept['specimen_md'] = 10
accept['specimen_fvds'] = 0.35
accept['specimen_b_beta'] = .1
accept['specimen_int_mad'] = 7
accept['specimen_dang'] = 10
accept['specimen_drats'] = 10
accept['specimen_Z'] = 10
#
# parse command line options
#
spc, BEG, END = "", "", ""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind + 1]
if '-fsp' in sys.argv:
ind = sys.argv.index('-fsp')
inspec = sys.argv[ind + 1]
if '-fcr' in sys.argv:
ind = sys.argv.index('-fcr')
critout = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = '.' + sys.argv[ind + 1]
if '-spc' in sys.argv:
ind = sys.argv.index('-spc')
spc = sys.argv[ind + 1]
if '-b' in sys.argv:
ind = sys.argv.index('-b')
BEG = int(sys.argv[ind + 1])
END = int(sys.argv[ind + 2])
if critout != "":
crit_data, file_type = pmag.magic_read(critout)
if pmagplotlib.verbose:
print "Acceptance criteria read in from ", critout
accept = {}
accept['specimen_int_ptrm_n'] = 2.0
for critrec in crit_data:
if critrec["pmag_criteria_code"] == "IE-SPEC":
for key in accept_keys:
if key not in critrec.keys():
accept[key] = -1
else:
accept[key] = float(critrec[key])
try:
open(inspec, 'rU')
PriorRecs, file_type = pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print file_type
print file_type, inspec, " is not a valid pmag_specimens file "
sys.exit()
for rec in PriorRecs:
if 'magic_software_packages' not in rec.keys():
rec['magic_software_packages'] = ""
except IOError:
PriorRecs = []
if pmagplotlib.verbose:
print "starting new specimen interpretation file: ", inspec
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()
backup = 0
# define figure numbers for arai, zijderveld and
# de-,re-magization diagrams
AZD = {}
AZD['deremag'], AZD['zijd'], AZD['arai'], AZD['eqarea'] = 1, 2, 3, 4
pmagplotlib.plot_init(AZD['arai'], 4, 4)
pmagplotlib.plot_init(AZD['zijd'], 4, 4)
pmagplotlib.plot_init(AZD['deremag'], 4, 4)
pmagplotlib.plot_init(AZD['eqarea'], 4, 4)
#
#
#
# get list of unique specimen names
#
CurrRec = []
sids = pmag.get_specs(meas_data)
# get plots for specimen s - default is just to step through arai diagrams
#
if spc != "": specimen = sids.index(spc)
while specimen < len(sids):
methcodes = []
if pmagplotlib.verbose and spc != "":
print sids[specimen], specimen + 1, 'of ', len(sids)
MeasRecs = []
s = sids[specimen]
datablock, trmblock = [], []
PmagSpecRec = {}
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["specimen_correction"] = 'u'
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"] == s:
MeasRecs.append(rec)
methods = rec["magic_method_codes"].split(":")
meths = []
for meth in methods:
meths.append(meth.strip()) # take off annoying spaces
methods = ""
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:
methcodes.append(meth.strip())
methods = methods + meth + ":"
methods = methods[:-1]
rec["magic_method_codes"] = methods
if "LP-PI-M" in meths: datablock.append(rec)
if "LP-MRM" in meths: trmblock.append(rec)
if len(trmblock) > 2 and inspec != "":
if Tinit == 0:
Tinit = 1
AZD['MRM'] = 4
pmagplotlib.plot_init(AZD['MRM'], 4, 4)
elif Tinit == 1:
pmagplotlib.clearFIG(AZD['MRM'])
if len(datablock) < 4:
if backup == 0:
specimen += 1
if pmagplotlib.verbose:
print 'skipping specimen - moving forward ', s
else:
specimen -= 1
if pmagplotlib.verbose:
print 'skipping specimen - moving backward ', s
#
# collect info for the PmagSpecRec dictionary
#
else:
rec = datablock[0]
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"]
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = ""
PmagSpecRec["magic_instrument_codes"] = rec[
"magic_instrument_codes"]
PmagSpecRec["measurement_step_unit"] = "J"
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec[
"magic_experiment_name"]
meths = rec["magic_method_codes"].split(':')
# sort data into types
if "LP-PI-M-D" in meths: # this is a double heating experiment
exp_type = "LP-PI-M-D"
elif "LP-PI-M-S" in meths:
exp_type = "LP-PI-M-S"
else:
print "experiment type not supported yet "
break
araiblock, field = pmag.sortmwarai(datablock, exp_type)
first_Z = araiblock[0]
first_I = araiblock[1]
GammaChecks = araiblock[-3]
ThetaChecks = araiblock[-2]
DeltaChecks = araiblock[-1]
if len(first_Z) < 3:
if backup == 0:
specimen += 1
if pmagplotlib.verbose:
print 'skipping specimen - moving forward ', s
else:
specimen -= 1
if pmagplotlib.verbose:
print 'skipping specimen - moving backward ', s
else:
backup = 0
zijdblock, units = pmag.find_dmag_rec(s, meas_data)
if exp_type == "LP-PI-M-D":
recnum = 0
print "ZStep Watts Dec Inc Int"
for plotrec in zijdblock:
if pmagplotlib.verbose:
print '%i %i %7.1f %7.1f %8.3e ' % (
recnum, plotrec[0], plotrec[1], plotrec[2],
plotrec[3])
recnum += 1
recnum = 1
if GammaChecks != "":
print "IStep Watts Gamma"
for gamma in GammaChecks:
if pmagplotlib.verbose:
print '%i %i %7.1f ' % (recnum, gamma[0],
gamma[1])
recnum += 1
if exp_type == "LP-PI-M-S":
if pmagplotlib.verbose:
print "IStep Watts Theta"
kk = 0
for theta in ThetaChecks:
kk += 1
print '%i %i %7.1f ' % (kk, theta[0], theta[1])
if pmagplotlib.verbose:
print "Watts Delta"
for delta in DeltaChecks:
print '%i %7.1f ' % (delta[0], delta[1])
pmagplotlib.plotAZ(AZD, araiblock, zijdblock, s, units[0])
if inspec != "":
if pmagplotlib.verbose:
print 'Looking up saved interpretation....'
found = 0
for k in range(len(PriorRecs)):
try:
if PriorRecs[k]["er_specimen_name"] == s:
found = 1
CurrRec.append(PriorRecs[k])
for j in range(len(araiblock[0])):
if float(araiblock[0][j][0]) == float(
PriorRecs[k]
["measurement_step_min"]):
start = j
if float(araiblock[0][j][0]) == float(
PriorRecs[k]
["measurement_step_max"]):
end = j
pars, errcode = pmag.PintPars(
araiblock, zijdblock, start, end)
pars['measurement_step_unit'] = "J"
del PriorRecs[
k] # put in CurrRec, take out of PriorRecs
if errcode != 1:
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
pars["er_specimen_name"] = s
if pmagplotlib.verbose:
print 'Saved interpretation: '
pars = pmag.scoreit(
pars, PmagSpecRec, accept, '', 0)
pmagplotlib.plotB(AZD, araiblock,
zijdblock, pars)
if len(trmblock) > 2:
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(
float(
trec['treatment_dc_field'])
)
TRMs.append(
float(trec[
'measurement_magn_moment'])
)
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt'][1]
) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(
AZD['MRM'], Bs, TRMs, Bp, Mp,
NLpars,
trec['magic_experiment_name'])
print npred
print 'Banc= ', float(
NLpars['banc']) * 1e6
if pmagplotlib.verbose:
print 'Banc= ', float(
NLpars['banc']) * 1e6
pmagplotlib.drawFIGS(AZD)
else:
print 'error on specimen ', s
except:
pass
if pmagplotlib.verbose and found == 0:
print ' None found :( '
if spc != "":
if BEG != "":
pars, errcode = pmag.PintPars(araiblock, zijdblock,
BEG, END)
pars['measurement_step_unit'] = "J"
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
pars["er_specimen_name"] = s
pars['specimen_grade'] = '' # ungraded
pmagplotlib.plotB(AZD, araiblock, zijdblock, pars)
if len(trmblock) > 2:
if inlt == 0:
donlt()
inlt = 1
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(
float(trec['measurement_magn_moment']))
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0], NLpars['xopt']
[1]) # predicted NRM for this field
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.saveP(AZD, files)
sys.exit()
if plots == 0:
ans = 'b'
while ans != "":
print """
s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
"""
ans = raw_input('Return for next specimen \n')
if ans == "":
specimen += 1
if ans == "d":
save_redo(PriorRecs, inspec)
CurrRec = []
pmagplotlib.plotAZ(AZD, araiblock, zijdblock, s,
units[0])
pmagplotlib.drawFIGS(AZD)
if ans == 'a':
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.saveP(AZD, files)
ans = ""
if ans == 'q':
print "Good bye"
sys.exit()
if ans == 'p':
specimen = specimen - 1
backup = 1
ans = ""
if ans == 's':
keepon = 1
spec = raw_input(
'Enter desired specimen name (or first part there of): '
)
while keepon == 1:
try:
specimen = sids.index(spec)
keepon = 0
except:
tmplist = []
for qq in range(len(sids)):
if spec in sids[qq]:
tmplist.append(sids[qq])
print specimen, " not found, but this was: "
print tmplist
spec = raw_input(
'Select one or try again\n ')
ans = ""
if ans == 'b':
if end == 0 or end >= len(araiblock[0]):
end = len(araiblock[0]) - 1
GoOn = 0
while GoOn == 0:
print 'Enter index of first point for calculation: ', '[', start, ']'
answer = raw_input('return to keep default ')
if answer != "": start = int(answer)
print 'Enter index of last point for calculation: ', '[', end, ']'
answer = raw_input('return to keep default ')
if answer != "":
end = int(answer)
if start >= 0 and start < len(araiblock[
0]) - 2 and end > 0 and end < len(
araiblock[0]) and start < end:
GoOn = 1
else:
print "Bad endpoints - try again! "
start, end = 0, len(araiblock)
s = sids[specimen]
pars, errcode = pmag.PintPars(
araiblock, zijdblock, start, end)
pars['measurement_step_unit'] = "J"
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
pars["er_specimen_name"] = s
pars = pmag.scoreit(pars, PmagSpecRec, accept, '',
0)
PmagSpecRec["measurement_step_min"] = '%8.3e' % (
pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"] = '%8.3e' % (
pars["measurement_step_max"])
PmagSpecRec["measurement_step_unit"] = "J"
PmagSpecRec["specimen_int_n"] = '%i' % (
pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"] = '%8.3e' % (
pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"] = '%8.3e ' % (
pars["specimen_int"])
PmagSpecRec["specimen_b"] = '%5.3f ' % (
pars["specimen_b"])
PmagSpecRec["specimen_q"] = '%5.1f ' % (
pars["specimen_q"])
PmagSpecRec["specimen_f"] = '%5.3f ' % (
pars["specimen_f"])
PmagSpecRec["specimen_fvds"] = '%5.3f' % (
pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"] = '%5.3f' % (
pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"] = '%7.1f' % (
pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"] = '%7.1f' % (
pars["specimen_Z"])
if pars["method_codes"] != "":
tmpcodes = pars["method_codes"].split(":")
for t in tmpcodes:
if t.strip() not in methcodes:
methcodes.append(t.strip())
PmagSpecRec["specimen_dec"] = '%7.1f' % (
pars["specimen_dec"])
PmagSpecRec["specimen_inc"] = '%7.1f' % (
pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"] = '-1'
PmagSpecRec["specimen_direction_type"] = 'l'
PmagSpecRec[
"direction_type"] = 'l' # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"] = '%7.1f ' % (
pars["specimen_dang"])
PmagSpecRec["specimen_drats"] = '%7.1f ' % (
pars["specimen_drats"])
PmagSpecRec["specimen_int_ptrm_n"] = '%i ' % (
pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"] = '%6.4f ' % (
pars["specimen_rsc"])
PmagSpecRec["specimen_md"] = '%i ' % (int(
pars["specimen_md"]))
if PmagSpecRec["specimen_md"] == '-1':
PmagSpecRec["specimen_md"] = ""
PmagSpecRec["specimen_b_sigma"] = '%5.3f ' % (
pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:
methcodes.append("IE-TT")
methods = ""
for meth in methcodes:
methods = methods + meth + ":"
PmagSpecRec["magic_method_codes"] = methods[:-1]
PmagSpecRec["specimen_description"] = comment
PmagSpecRec[
"magic_software_packages"] = version_num
pmagplotlib.plotAZ(AZD, araiblock, zijdblock, s,
units[0])
pmagplotlib.plotB(AZD, araiblock, zijdblock, pars)
if len(trmblock) > 2:
blab = field
best = pars["specimen_int"]
Bs, TRMs = [], []
for trec in trmblock:
Bs.append(float(
trec['treatment_dc_field']))
TRMs.append(
float(trec['measurement_magn_moment']))
NLpars = nlt.NLtrm(
Bs, TRMs, best, blab, 0
) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp, Bp = [], []
for k in range(int(max(Bs) * 1e6)):
Bp.append(float(k) * 1e-6)
npred = nlt.TRM(
Bp[-1], NLpars['xopt'][0],
NLpars['xopt']
[1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(
AZD['MRM'], Bs, TRMs, Bp, Mp, NLpars,
trec['magic_experiment_name'])
print 'Banc= ', float(NLpars['banc']) * 1e6
pmagplotlib.drawFIGS(AZD)
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars[
"specimen_b"]
saveit = raw_input(
"Save this interpretation? [y]/n \n")
if saveit != 'n':
specimen += 1
PriorRecs.append(
PmagSpecRec) # put back an interpretation
save_redo(PriorRecs, inspec)
ans = ""
else:
specimen += 1
if fmt != ".pmag":
basename = s + '_microwave' + fmt
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['deremag'] = 'DeReMag Plot'
titles['zijd'] = 'Zijderveld Plot'
titles['arai'] = 'Arai Plot'
AZD = pmagplotlib.addBorders(
AZD, titles, black, purple)
pmagplotlib.saveP(AZD, files)
# pmagplotlib.combineFigs(s,files,3)
if len(CurrRec) > 0:
for rec in CurrRec:
PriorRecs.append(rec)
CurrRec = []
if plots != 1:
ans = raw_input(" Save last plot? 1/[0] ")
if ans == "1":
if fmt != ".pmag":
files = {}
for key in AZD.keys():
files[key] = s + '_' + key + fmt
pmagplotlib.saveP(AZD, files)
if len(CurrRec) > 0:
PriorRecs.append(CurrRec) # put back an interpretation
if len(PriorRecs) > 0:
save_redo(PriorRecs, inspec)
print 'Updated interpretations saved in ', inspec
if pmagplotlib.verbose:
print "Good bye"
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
-DM [2,3] define data model
"""
dirlist=['./']
dir_path=os.getcwd()
names=os.listdir(dir_path)
for n in names:
if 'Location' in n:
dirlist.append(n)
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
else: fmt='png'
if '-f' in sys.argv:
ind=sys.argv.index("-f")
filelist=[sys.argv[ind+1]]
else:
filelist=os.listdir(dir_path)
new_model=0
if '-DM' in sys.argv:
ind=sys.argv.index("-DM")
data_model=sys.argv[ind+1]
if data_model=='3': new_model=1
if new_model:
samp_file='samples.txt'
azimuth_key='azimuth'
meas_file='measurements.txt'
loc_key='location'
method_key='method_codes'
dec_key='dir_dec'
inc_key='dir_inc'
Mkeys=['magnitude','magn_moment','magn_volume','magn_mass']
results_file='sites.txt'
tilt_key='direction_tilt_correction'
hyst_file='specimens.txt'
aniso_file='specimens.txt'
else:
new_model=0
samp_file='er_samples.txt'
azimuth_key='sample_azimuth'
meas_file='magic_measurements.txt'
loc_key='er_location_name'
method_key='magic_method_codes'
dec_key='measurement_dec'
inc_key='measurement_inc'
Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
results_file='pmag_results.txt'
tilt_key='tilt_correction'
hyst_file='rmag_hysteresis'
aniso_file='rmag_anisotropy'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
for loc in dirlist:
print('working on: ',loc)
os.chdir(loc) # change working directories to each location
crd='s'
print(samp_file)
if samp_file in filelist: # find coordinate systems
print('found sample file')
samps,file_type=pmag.magic_read(samp_file) # read in data
Srecs=pmag.get_dictitem(samps,azimuth_key,'','F')# get all none blank sample orientations
if len(Srecs)>0:
crd='g'
if meas_file in filelist: # start with measurement data
print('working on measurements data')
data,file_type=pmag.magic_read(meas_file) # read in data
if loc == './': data=pmag.get_dictitem(data,loc_key,'','T') # get all the blank location names from data file
# looking for zeq_magic possibilities
AFZrecs=pmag.get_dictitem(data,method_key,'LT-AF-Z','has')# get all none blank method codes
TZrecs=pmag.get_dictitem(data,method_key,'LT-T-Z','has')# get all none blank method codes
MZrecs=pmag.get_dictitem(data,method_key,'LT-M-Z','has')# get all none blank method codes
Drecs=pmag.get_dictitem(data,dec_key,'','F') # get all dec measurements
Irecs=pmag.get_dictitem(data,inc_key,'','F') # get all inc measurements
for key in Mkeys:
Mrecs=pmag.get_dictitem(data,key,'','F') # get intensity data
if len(Mrecs)>0:break
if len(AFZrecs)>0 or len(TZrecs)>0 or len(MZrecs)>0 and len(Drecs)>0 and len(Irecs)>0 and len(Mrecs)>0: # potential for stepwise demag curves
if new_model:
CMD = 'zeq_magic3.py -fsp specimens.txt -sav -fmt '+fmt+' -crd '+crd
else:
CMD='zeq_magic.py -fsp pmag_specimens.txt -sav -fmt '+fmt+' -crd '+crd
print(CMD)
os.system(CMD)
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data,method_key,'LP-PI-TRM','has'))>0:
if new_model:
CMD= 'thellier_magic3.py -fsp specimens.txt -sav -fmt '+fmt
else:
CMD= 'thellier_magic.py -fsp pmag_specimens.txt -sav -fmt '+fmt
print(CMD)
os.system(CMD)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data,method_key,'LP-HYS','has'))>0: # find hyst experiments
if new_model:
CMD= 'quick_hyst3.py -sav -fmt '+fmt
else:
CMD= 'quick_hyst.py -sav -fmt '+fmt
print(CMD)
os.system(CMD)
if results_file in filelist: # start with measurement data
data,file_type=pmag.magic_read(results_file) # read in data
print('number of datapoints: ',len(data))
if loc == './': data=pmag.get_dictitem(data,loc_key,':','has') # get all the concatenated location names from data file
print('number of datapoints: ',len(data) ,loc)
if new_model:
print('working on site directions')
dec_key='dir_dec'
inc_key='dir_inc'
int_key='int_abs'
else:
print('working on results directions')
dec_key='average_dec'
inc_key='average_inc'
int_key='average_int'
SiteDIs=pmag.get_dictitem(data,dec_key,"",'F') # find decs
SiteDIs=pmag.get_dictitem(SiteDIs,inc_key,"",'F') # find decs and incs
SiteDIs=pmag.get_dictitem(SiteDIs,'data_type','i','has') # only individual results - not poles
print('number of directions: ',len(SiteDIs))
SiteDIs_t=pmag.get_dictitem(SiteDIs,tilt_key,'100','T')# tilt corrected coordinates
print('number of tilt corrected directions: ',len(SiteDIs))
SiteDIs_g=pmag.get_dictitem(SiteDIs,tilt_key,'0','T')# geographic coordinates
SiteDIs_s=pmag.get_dictitem(SiteDIs,'tilt_correction','-1','T')# sample coordinates
SiteDIs_x=pmag.get_dictitem(SiteDIs,'tilt_correction','','T')# no coordinates
if len(SiteDIs_t)>0 or len(SiteDIs_g) >0 or len(SiteDIs_s)>0 or len(SiteDIs_x)>0:
CRD=""
if len(SiteDIs_t)>0:
CRD=' -crd t'
elif len(SiteDIs_g )>0:
CRD=' -crd g'
elif len(SiteDIs_s )>0:
CRD=' -crd s'
if new_model:
CMD= 'eqarea_magic3.py -sav -crd t -fmt '+fmt +CRD
else:
CMD= 'eqarea_magic.py -sav -crd t -fmt '+fmt +CRD
print(CMD)
os.system(CMD)
print('working on VGP map')
VGPs=pmag.get_dictitem(SiteDIs,'vgp_lat',"",'F') # are there any VGPs?
if len(VGPs)>0: # YES!
os.system('vgpmap_magic.py -prj moll -res c -sym ro 5 -sav -fmt png')
print('working on intensities')
if not new_model:
CMD='magic_select.py -f '+results_file+' -key data_type i T -F tmp.txt'
os.system(CMD)
infile=' tmp.txt'
else: infile=results_file
print(int_key)
CMD='magic_select.py -key '+int_key +' 0. has -F tmp1.txt -f '+infile
os.system(CMD)
CMD="grab_magic_key.py -f tmp1.txt -key "+int_key+ " | awk '{print $1*1e6}' >tmp2.txt"
os.system(CMD)
data,file_type=pmag.magic_read('tmp1.txt') # read in data
if new_model:
locations=pmag.get_dictkey(data,loc_key,"")
else:
locations=pmag.get_dictkey(data,loc_key+'s',"")
histfile='LO:_'+locations[0]+'_intensities_histogram:_.'+fmt
os.system("histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " +histfile)
print("histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " +histfile)
os.system('rm tmp*.txt')
if hyst_file in filelist: # start with measurement data
print('working on hysteresis')
data,file_type=pmag.magic_read(hyst_file) # read in data
if loc == './': data=pmag.get_dictitem(data,loc_key,'','T') # get all the blank location names from data file
hdata=pmag.get_dictitem(data,'hysteresis_bcr','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_mr_moment','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_ms_moment','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_bc','','F') # there are data for a dayplot
if len(hdata)>0:
print('dayplot_magic.py -sav -fmt '+fmt)
os.system('dayplot_magic.py -sav -fmt '+fmt)
if aniso_file in filelist: # do anisotropy plots if possible
print('working on anisotropy')
data,file_type=pmag.magic_read(aniso_file) # read in data
if loc == './': data=pmag.get_dictitem(data,loc_key,'','T') # get all the blank location names from data file
sdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','-1','T') # get specimen coordinates
gdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','0','T') # get specimen coordinates
tdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','100','T') # get specimen coordinates
CRD=""
if new_model:
CMD= 'aniso_magic3.py -x -B -sav -fmt '+fmt
else:
CMD= 'aniso_magic.py -x -B -sav -fmt '+fmt
if len(sdata)>3:
CMD=CMD+' -crd s'
print(CMD)
os.system(CMD)
if len(gdata)>3:
CMD=CMD+' -crd g'
print(CMD)
os.system(CMD)
if len(tdata)>3:
CMD=CMD+' -crd t'
print(CMD)
os.system(CMD)
if loc!='./':os.chdir('..') # change working directories to each location
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
"""
dirlist = ['./']
dir_path = os.getcwd()
names = os.listdir(dir_path)
for n in names:
if 'Location' in n:
dirlist.append(n)
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
else:
fmt = 'png'
if '-f' in sys.argv:
ind = sys.argv.index("-f")
filelist = [sys.argv[ind + 1]]
else:
filelist = os.listdir(dir_path)
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
for loc in dirlist:
print('working on: ', loc)
os.chdir(loc) # change working directories to each location
crd = 's'
if 'er_samples.txt' in filelist: # find coordinate systems
samps, file_type = pmag.magic_read(
'er_samples.txt') # read in data
Srecs = pmag.get_dictitem(
samps, 'sample_azimuth', '',
'F') # get all none blank sample orientations
if len(Srecs) > 0:
crd = 'g'
if 'magic_measurements.txt' in filelist: # start with measurement data
print('working on measurements data')
data, file_type = pmag.magic_read(
'magic_measurements.txt') # read in data
if loc == './':
data = pmag.get_dictitem(
data, 'er_location_name', '',
'T') # get all the blank location names from data file
# looking for zeq_magic possibilities
AFZrecs = pmag.get_dictitem(
data, 'magic_method_codes', 'LT-AF-Z',
'has') # get all none blank method codes
TZrecs = pmag.get_dictitem(
data, 'magic_method_codes', 'LT-T-Z',
'has') # get all none blank method codes
MZrecs = pmag.get_dictitem(
data, 'magic_method_codes', 'LT-M-Z',
'has') # get all none blank method codes
Drecs = pmag.get_dictitem(data, 'measurement_dec', '',
'F') # get all dec measurements
Irecs = pmag.get_dictitem(data, 'measurement_inc', '',
'F') # get all dec measurements
Mkeys = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass'
]
for key in Mkeys:
Mrecs = pmag.get_dictitem(data, key, '',
'F') # get intensity data
if len(Mrecs) > 0: break
if len(AFZrecs) > 0 or len(TZrecs) > 0 or len(MZrecs) > 0 and len(
Drecs) > 0 and len(Irecs) > 0 and len(
Mrecs) > 0: # potential for stepwise demag curves
print('zeq_magic.py -fsp pmag_specimens.txt -sav -fmt ' + fmt +
' -crd ' + crd)
os.system('zeq_magic.py -sav -fmt ' + fmt + ' -crd ' + crd)
# looking for thellier_magic possibilities
if len(
pmag.get_dictitem(data, 'magic_method_codes', 'LP-PI-TRM',
'has')) > 0:
print('thellier_magic.py -fsp pmag_specimens.txt -sav -fmt ' +
fmt)
os.system('thellier_magic.py -sav -fmt ' + fmt)
# looking for hysteresis possibilities
if len(
pmag.get_dictitem(data, 'magic_method_codes', 'LP-HYS',
'has')) > 0: # find hyst experiments
print('quick_hyst.py -sav -fmt ' + fmt)
os.system('quick_hyst.py -sav -fmt ' + fmt)
if 'pmag_results.txt' in filelist: # start with measurement data
data, file_type = pmag.magic_read(
'pmag_results.txt') # read in data
print('number of datapoints: ', len(data))
if loc == './':
data = pmag.get_dictitem(
data, 'er_location_names', ':', 'has'
) # get all the concatenated location names from data file
print('number of datapoints: ', len(data), loc)
print('working on pmag_results directions')
SiteDIs = pmag.get_dictitem(data, 'average_dec', "",
'F') # find decs
print('number of directions: ', len(SiteDIs))
SiteDIs = pmag.get_dictitem(SiteDIs, 'average_inc', "",
'F') # find decs and incs
print('number of directions: ', len(SiteDIs))
SiteDIs = pmag.get_dictitem(
SiteDIs, 'data_type', 'i',
'has') # only individual results - not poles
print('number of directions: ', len(SiteDIs))
SiteDIs_t = pmag.get_dictitem(SiteDIs, 'tilt_correction', '100',
'T') # tilt corrected coordinates
print('number of directions: ', len(SiteDIs))
if len(SiteDIs_t) > 0:
print('eqarea_magic.py -sav -crd t -fmt ' + fmt)
os.system('eqarea_magic.py -sav -crd t -fmt ' + fmt)
elif len(SiteDIs) > 0 and 'tilt_correction' not in SiteDIs[0].keys(
):
print('eqarea_magic.py -sav -fmt ' + fmt)
os.system('eqarea_magic.py -sav -fmt ' + fmt)
else:
SiteDIs_g = pmag.get_dictitem(SiteDIs, 'tilt_correction', '0',
'T') # geographic coordinates
if len(SiteDIs_g) > 0:
print('eqarea_magic.py -sav -crd g -fmt ' + fmt)
os.system('eqarea_magic.py -sav -crd g -fmt ' + fmt)
else:
SiteDIs_s = pmag.get_dictitem(SiteDIs, 'tilt_correction',
'-1',
'T') # sample coordinates
if len(SiteDIs_s) > 0:
print('eqarea_magic.py -sav -crd s -fmt ' + fmt)
os.system('eqarea_magic.py -sav -crd s -fmt ' + fmt)
else:
SiteDIs_x = pmag.get_dictitem(SiteDIs,
'tilt_correction', '',
'T') # no coordinates
if len(SiteDIs_x) > 0:
print('eqarea_magic.py -sav -fmt ' + fmt)
os.system('eqarea_magic.py -sav -fmt ' + fmt)
print('working on pmag_results VGP map')
VGPs = pmag.get_dictitem(SiteDIs, 'vgp_lat', "",
'F') # are there any VGPs?
if len(VGPs) > 0: # YES!
os.system(
'vgpmap_magic.py -prj moll -res c -sym ro 5 -sav -fmt png')
print('working on pmag_results intensities')
os.system(
'magic_select.py -f pmag_results.txt -key data_type i T -F tmp.txt'
)
os.system(
'magic_select.py -f tmp.txt -key average_int 0. has -F tmp1.txt'
)
os.system(
"grab_magic_key.py -f tmp1.txt -key average_int | awk '{print $1*1e6}' >tmp2.txt"
)
data, file_type = pmag.magic_read('tmp1.txt') # read in data
locations = pmag.get_dictkey(data, 'er_location_names', "")
histfile = 'LO:_' + locations[0] + '_intensities_histogram:_.' + fmt
os.system(
"histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F "
+ histfile)
print(
"histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F "
+ histfile)
os.system('rm tmp*.txt')
if 'rmag_hysteresis.txt' in filelist: # start with measurement data
print('working on rmag_hysteresis')
data, file_type = pmag.magic_read(
'rmag_hysteresis.txt') # read in data
if loc == './':
data = pmag.get_dictitem(
data, 'er_location_name', '',
'T') # get all the blank location names from data file
hdata = pmag.get_dictitem(data, 'hysteresis_bcr', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_mr_moment', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_ms_moment', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_bc', '',
'F') # there are data for a dayplot
if len(hdata) > 0:
print('dayplot_magic.py -sav -fmt ' + fmt)
os.system('dayplot_magic.py -sav -fmt ' + fmt)
#if 'er_sites.txt' in filelist: # start with measurement data
# print 'working on er_sites'
#os.system('basemap_magic.py -sav -fmt '+fmt)
if 'rmag_anisotropy.txt' in filelist: # do anisotropy plots if possible
print('working on rmag_anisotropy')
data, file_type = pmag.magic_read(
'rmag_anisotropy.txt') # read in data
if loc == './':
data = pmag.get_dictitem(
data, 'er_location_name', '',
'T') # get all the blank location names from data file
sdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction', '-1',
'T') # get specimen coordinates
gdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction', '0',
'T') # get specimen coordinates
tdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction',
'100', 'T') # get specimen coordinates
if len(sdata) > 3:
print('aniso_magic.py -x -B -crd s -sav -fmt ' + fmt)
os.system('aniso_magic.py -x -B -crd s -sav -fmt ' + fmt)
if len(gdata) > 3:
os.system('aniso_magic.py -x -B -crd g -sav -fmt ' + fmt)
if len(tdata) > 3:
os.system('aniso_magic.py -x -B -crd t -sav -fmt ' + fmt)
if loc != './':
os.chdir('..') # change working directories to each location
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
customize_criteria.py
DESCRIPTION
Allows user to specify acceptance criteria, saves them in pmag_criteria.txt
SYNTAX
customize_criteria.py [-h][command line options]
OPTIONS
-h prints help message and quits
-f IFILE, reads in existing criteria
-F OFILE, writes to pmag_criteria format file
DEFAULTS
IFILE: pmag_criteria.txt
OFILE: pmag_criteria.txt
OUTPUT
creates a pmag_criteria.txt formatted output file
"""
infile,critout="","pmag_criteria.txt"
# parse command line options
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
infile=sys.argv[ind+1]
crit_data,file_type=pmag.magic_read(infile)
if file_type!='pmag_criteria':
print 'bad input file'
print main.__doc__
sys.exit()
print "Acceptance criteria read in from ", infile
if '-F' in sys.argv:
ind=sys.argv.index('-F')
critout=sys.argv[ind+1]
Dcrit,Icrit,nocrit=0,0,0
custom='1'
crit=raw_input(" [0] Use no acceptance criteria?\n [1] Use default criteria\n [2] customize criteria \n ")
if crit=='0':
print 'Very very loose criteria saved in ',critout
crit_data=pmag.default_criteria(1)
pmag.magic_write(critout,crit_data,'pmag_criteria')
sys.exit()
crit_data=pmag.default_criteria(0)
if crit=='1':
print 'Default criteria saved in ',critout
pmag.magic_write(critout,crit_data,'pmag_criteria')
sys.exit()
CritRec=crit_data[0]
crit_keys=CritRec.keys()
crit_keys.sort()
print "Enter new threshold value.\n Return to keep default.\n Leave blank to not use as a criterion\n "
for key in crit_keys:
if key!='pmag_criteria_code' and key!='er_citation_names' and key!='criteria_definition' and CritRec[key]!="":
print key, CritRec[key]
new=raw_input('new value: ')
if new != "": CritRec[key]=(new)
pmag.magic_write(critout,[CritRec],'pmag_criteria')
print "Criteria saved in pmag_criteria.txt"
